Index (Geneious Public API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

A

AbstractPluginDocument - Class in com.biomatters.geneious.publicapi.documents: This class provides a "Field based" implementation of a Plugin documents.
AbstractPluginDocument(Date) - Constructor for class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: Construct a new document with a given time of creation.
AbstractPluginDocument(Date, URN) - Constructor for class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: Construct a new document with a given URN and time of creation.
AbstractPluginDocument() - Constructor for class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: Create a new document with a creation date taken from system clock.
acceptsChangesAfterRetrieveCompletes(SimpleListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: If a database service wishes to make changes to the result of a retrieve after the retrieve method has returned then it should call this method first.
ACCESSION_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Visible, non-editable field representing a document's accession.
ACTION_MAP_KEY_COPY - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Standard Java Action map key for Edit -> Copy.
ACTION_MAP_KEY_CUT - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Standard Java Action map key for Edit -> Cut.
ACTION_MAP_KEY_DELETE - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Standard Java Action map key for Edit -> Delete.
ACTION_MAP_KEY_PASTE - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Standard Java Action map key for Edit -> Paste.
ACTION_MAP_KEY_REDO - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Geneious Action map key for Edit -> Redo.
ACTION_MAP_KEY_SELECT_ALL - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Standard Java Action map key for Edit -> Select All on anything but a JTable.
ACTION_MAP_KEY_SELECT_ALL_TABLE - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Standard Java Action map key for Edit -> Select All on a JTable.
ACTION_MAP_KEY_UNDO - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Geneious Action map key for Edit -> Undo.
actionPerformed(AnnotatedPluginDocument[]) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentAction: Perform a document action.
actionPerformed(ActionEvent) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction.Divider
actionPerformed(ActionEvent) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction.SubMenu
actionPerformed(ActionEvent) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction.ToggleAction
ActionProvider - Class in com.biomatters.geneious.publicapi.plugin: May be supplied by a DocumentViewer to support standard actions (such as copy and paste) or any additional custom actions.
ActionProvider(ActionProvider) - Constructor for class com.biomatters.geneious.publicapi.plugin.ActionProvider: Create a wrapper ActionProvider that delegates all methods to an internal ActionProvider.
ActionProvider() - Constructor for class com.biomatters.geneious.publicapi.plugin.ActionProvider: Default constructor.
actionsChanged() - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceListener: Notify the program that the actions returned by GeneiousService.getActionsAlwaysEnabled() or GeneiousService.getActionsEnabledWhenServiceSelected() have changed since the service was initialized or this was last called.
actionToggled(ActionEvent, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction.ToggleAction: Called when the action is performed, indicating that the selected state of the action has changed.
add(Component, Object) - Method in class com.biomatters.geneious.publicapi.components.DialogButtonPanel
add(PluginDocument, Map<String, Object>) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: A wrapper method that forwards its arguments to RetrieveCallback._add(com.biomatters.geneious.publicapi.documents.PluginDocument, java.util.Map) only if this retrieval hasn't been canceled.
add(AnnotatedPluginDocument, Map<String, Object>) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: A wrapper method that forwards its arguments to RetrieveCallback._add(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, java.util.Map) only if this retrieval hasn't been canceled.
add(T, long) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ExternalSort: Adds a new element to sort
add(Runnable) - Static method in class com.biomatters.geneious.publicapi.utilities.CallSoon: Invokes this runnable soon (like using SwingUtilities.invokeLater(Runnable)) in the event dispatch thread.
add(Runnable, long, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.CallSoon: Invokes this runnable soon (like using SwingUtilities.invokeLater(Runnable)) in the event dispatch thread.
add(Runnable, long, boolean, CallSoon.EnabledProvider) - Static method in class com.biomatters.geneious.publicapi.utilities.CallSoon: Invoke this runnable soon in the Event dispatch thread.
add(Object, Runnable) - Static method in class com.biomatters.geneious.publicapi.utilities.GarbageCollectionNotifier: Sets things up so that soon after this object is garbage collected, the given Runnable is invoked.
add(int) - Method in class com.biomatters.geneious.publicapi.utilities.IntList.Array: Adds a new element to the end of the list
add(T) - Method in class com.biomatters.geneious.publicapi.utilities.MultiThreadedProcessingSystem: Adds a new entry to be processed.
add(E) - Method in class com.biomatters.geneious.publicapi.utilities.WeakReferenceList: Adds a weak reference to the given object
add(SimpleListener) - Method in class com.biomatters.geneious.publicapi.utilities.WeakSimpleListenerManager
addAction(GeneiousAction) - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: Add an action to the toolbar.
addAction(GeneiousAction, boolean) - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: Add an action to the toolbar.
addAction(GeneiousAction, boolean, boolean) - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: Add an action to the toolbar.
addActionListener(ActionListener) - Method in class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption: Adds a listener to be notified when this button option is clicked
addActionListener(ActionListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionGrabOption: Adds a listener to be notified when the button has been clicked on.
addActionsChangedListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: if the action provider may change the actions it provides at some point then it should notify all of the listeners that have been added using this function.
addActiveOptionsChangedListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.PluginPreferences: Adds a listener to be notified when the options returned by PluginPreferences.getActiveOptions() have changed.
addAdditionalAction(GeneiousAction) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Adds an additional action that this service will provide via WritableDatabaseService.getActionsEnabledWhenServiceSelected()
addAdditionalHelp(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Add some additional help to append to the end of the standard help this folder returned from WritableDatabaseService.getHelp()
addAlignmentReferenceSequence(SequenceDocument, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Adds a reference sequence when building an alignment.
addAminoAcidSequence(AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: Adds an amino acid sequence to this list that is wrapped inside an AnnotatedPluginDocument.
addAminoAcidSequence(AminoAcidSequenceDocument) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
addAminoAcidSequence(AminoAcidSequenceDocument) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceListDocument: Adds the given amino acid sequence to the end of the list of amino acid sequences in this document
Note that using this method will require loading the entire sequence list into memory, which might not be possible on large sequence lists.
addAndReturnGeneratedDocuments(List<AnnotatedPluginDocument>, boolean, List<AnnotatedPluginDocument>, WritableDatabaseService) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Adds a list of documents that have just been generated to Geneious so that appear in the users local database and so that they become visible in the document table.
addAndReturnGeneratedDocuments(List<AnnotatedPluginDocument>, boolean, List<AnnotatedPluginDocument>) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Adds a list of documents that have just been generated to Geneious so that appear in the users local database and returns the newly added documents.
addAnnotationToAdd(SequenceAnnotation) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Adds an annotation to be added to the sequence once this annotation generator finishes.
addAnnotationToRemove(SequenceAnnotation) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Adds an annotation to the list of annotations to be removed from the sequence once this annotation generator finishes.
addAssemblyReportText(String) - Method in class com.biomatters.geneious.publicapi.plugin.Assembler.Callback: Adds some text to be included in the assembly report (if the user chooses to generate or display one).
addBooleanOption(String, String, Boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add an option that stores a Boolean and is represented graphically as a check box.
addButton(AbstractButton, boolean) - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: Deprecated.
use GeneiousActionToolbar.addAction(com.biomatters.geneious.publicapi.plugin.GeneiousAction) or GeneiousActionToolbar.addAction(com.biomatters.geneious.publicapi.plugin.GeneiousAction, boolean) instead.
addButtonOption(String, String, String, Icon, int) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Adds an option that is represented by a button, and may have actions attached to it which are activated when the user clicks the button (see Options.ButtonOption.addActionListener(java.awt.event.ActionListener)).
addButtonOption(String, String, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Adds an option that is represented by a button, and may have actions attached to it which are activated when the user clicks the button (see Options.ButtonOption.addActionListener(java.awt.event.ActionListener)).
addChangeListener(ChangeListener) - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: Add a listener to be notified when the zoom changes
addChangeListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.FolderView: Add a listener which is notified whenever the contents of the folder view folder is changed.
addChangeListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Add a listener which will be notified when any changes are made to this field (eg.
addChangeListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Adds a listener to be notified when the values of any properties change.
addChangelistener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousPreference: Deprecated.

Add a listener to this preference which will get fired whenever the current value of the preference is changed.
addChangeListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.Options: add a listener to be notified when the value of any option changes The listener is also notified if some options requires an active license, and the licence type changes.
addChangeListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions: Add a listener to be notified when any of the values or number of values for these multiple options change.
addChangeListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Add a listener to be notified when the value of this option changes.
addChildOptions(String, String, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Creates, adds and returns some child options.
addChildOptions(String, String, String, Options) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Calls addChildOptions(name,label,description,childOptions,false).
addChildOptions(String, String, String, Options, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Adds a set of existing Options as child options of this Options.
addChildOptionsDependent(Options, ValueType, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Make the enabled state of some child options depend on the current value of this option.
addChildOptionsPageChooser(String, String, List<String>, Options.PageChooserType, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Makes all previously added child options available via a list of tab buttons.
addCollapsibleChildOptions(String, String, String, Options, boolean, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add child options that can be expanded and collapsed.
addComboBoxOption(String, String, List<? extends T>, T) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add a new ComboBoxOption.
addComboBoxOption(String, String, T[], T) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add a new ComboBoxOption.
addComponent(JComponent, boolean) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Add a component without a label.
addComponentLocationChangedListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension: Adds a listener to be notified when the value returned from SequenceViewerExtension.getComponentLocation() changes
addComponentPositionActions(GeneiousActionToolbar, SequenceViewerExtension.ComponentLocation...) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension: Adds little buttons to a toolbar to control the location (see SequenceViewerExtension.getComponentLocation()) of the component (see SequenceViewerExtension.getComponent()) in the sequence viewer.
addComponentPositionPopInOrOutAction(GeneiousActionToolbar, SequenceViewerExtension.ComponentLocation, SequenceViewerExtension.ComponentLocation) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension: Adds a little button to the toolbar to control the location (see SequenceViewerExtension.getComponentLocation()) of the component (see SequenceViewerExtension.getComponent()) in the sequence viewer.
addComponentWithLabel(String, JComponent, boolean) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Add a component with a label.
addComponentWithLabel(JLabel, JComponent, boolean) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Add a component with a label.
addContigDocument(SequenceAlignmentDocument, NucleotideSequenceDocument, boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.Assembler.Callback: Adds a contig generated by this assembler.
addContigReferenceSequence(SequenceDocument) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Adds a sequence as the contig reference sequence {see @link #getContigReferenceSequenceIndex()}.
addCustomComponent(GeneiousActionToolbar.CustomToolbarComponent) - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: Adds a custom component to the toolbar.
addCustomComponent(JComponent) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Adds a custom component that will be laid out along with all the standard options.
addCustomComponent(Options.ComponentCreator) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Adds a custom component that will be laid out along with all the standard options.
addCustomOption(OptionType) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add a custom option.
addDatabase(File, String, Options, ProgressListener, DatabaseService.SequenceSearchQueryType) - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService: Add a new sequence database to the service from a file on disk.
addDatabase(AnnotatedPluginDocument[], String, Options, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService: Add a new sequence database to the service from a selection of documents in Geneious.
addDatabaseServiceListener(DatabaseServiceListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: DatabaseServiceListener has several methods for the database service to notify the program of changes.
addDatabaseServiceListener(DatabaseServiceListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: A sub-class must not override this, but should instead use WritableDatabaseService.getDatabaseServiceListeners() as this class relies on WritableDatabaseService.getDatabaseServiceListeners().
addDateOption(String, String, Date) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add an option that stores a Date (day, month and year only) and is displayed graphically to the user as a set of 3 spinners together with a button that opens a new dialog for nicer date selection from a calendar style view.
addDefaultsRestoredListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.Options: add a listener to be notified when the options are restored to their defaults (e.g.
addDependent(Options.Option, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.BooleanOption: Makes another option's enabled state depend on this boolean option being on or off.
addDependent(Options.Option, boolean, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.BooleanOption: Makes another option's enabled state depend on this boolean option being on or off.
addDependent(Options.Option, ValueType) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Makes another option's enabled state depend on the current value of this option.
addDependent(ValueType, Options.Option, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.RadioOption: Adds a dependent option that will be enabled when the radio button associated with the OptionValue is selected, and disabled when it is not.
addDependent(ValueType, Options, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.RadioOption: Adds a dependent option that will be enabled when the radio button associated with the OptionValue is selected, and disabled when it is not.
addDependentChildOptions(Options, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption: The child options passed into this method will not be displayed inline in the options panel.
addDescendantOperationRecord(URN) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Adds a record of an operation where this document was an input document to the operation.
addDisplayableField(DocumentField) - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: adds a displayable field to the document that is stored with the documents.
addDivider() - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Add a 1 pixel high, gray horizontal line which divides the components vertically.
addDivider(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add a new divider that is displayed between options when the options are graphically presented to the user.
addDividerWithLabel(String) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Add a 1 pixel high, gray horizontal line which divides the components vertically.
addDocument(AnnotatedPluginDocument, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.Assembler.Callback: Adds a document generated by this assembler.
addDocument(PluginDocument) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.ImportCallback: Report back one imported PluginDocument.
addDocument(AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.ImportCallback: Report back one imported AnnotatedPluginDocument.
addDocument(AnnotatedPluginDocument, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.ImportCallback: Report back one imported AnnotatedPluginDocument.
addDocument(AnnotatedPluginDocument, ProgressListener, String) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.ImportCallback: Report back one imported AnnotatedPluginDocument.
addDocument(PluginDocument, boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback: returns a document from the operaiton while the operation is still in progress.
addDocument(AnnotatedPluginDocument, boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback: returns a document from the operation while the operation is still in progress.
addDocument(AnnotatedPluginDocument, boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback.Wrapper
addDocumentCopy(AnnotatedPluginDocument, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Add a copy of this document to this database.
addDocumentCopyWithProperties(AnnotatedPluginDocument, ProgressListener, Map<String, Object>) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Equivalent to addDocumentCopyWithProperties(document, prorgress, properties, null)
addDocumentCopyWithProperties(AnnotatedPluginDocument, ProgressListener, Map<String, Object>, URN) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Add a copy of this document to this database with additional properties that will show up as associated with this document on any future queries while the document resides in this folder.
addDocumentFieldToSet(DocumentFieldAndValue) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Adds a document field and value (or replaces an existing note with the same Object.getClass()) to the sequence.
addDocumentNoteToSet(DocumentNote) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Adds (or replaces an existing note with the same DocumentNote.getNoteTypeCode()) on the sequence.
addDocumentProperties(URN, Map<String, Object>) - Method in class com.biomatters.geneious.publicapi.databaseservice.FolderView: Add a set of properties associated with a document.
addDocumentProperties(Map<URN, Map<String, Object>>) - Method in class com.biomatters.geneious.publicapi.databaseservice.FolderView: Update search properties for several documents at once.
addDocumentSelectionOption(String, String, DocumentSelectionOption.FolderOrDocuments, DocumentType, List<DocumentField>, boolean, List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.plugin.Options: An option to allow the user to select a number of documents of a particular type from their local database.
addDocumentsUpdatedListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.documents.DocumentSearchCache: Add a listener to be fired when the list of documents in the cache changes (either because new documents are added or old documents have been deleted).
addDoubleOption(String, String, Double, Double, Double) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add an option that stores an Double and is displayed graphically to the user as a single line text field with a spinner (up and down arrow) on the right-hand side
For information on what the initial value of this option is set to see addStringOption.
addDoubleOption(String, String, Double) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add an option that stores an Double and is displayed graphically to the user as a single line text field with a spinner (up and down arrow) on the right-hand side
For information on what the initial value of this option is set to see addStringOption.
addEditableComboBoxOption(String, String, String, String[]) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add an option that stores a String that is displayed graphically to the user as a single line text field.
addEditableComboBoxOption(String, String, String, String[], int) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add an option that stores a String that is displayed graphically to the user as a single line text field.
addEditMenuSupport(JTextComponent) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Links a JTextComponent to the Edit menu actions Cut, Copy, Paste and Select All.
addExecutableFileSelectionOption(String, String, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Adds an ExecutableFileSelectionOption where the default executable path is just the filename without a path component, i.e.
addExecutableFileSelectionOption(String, String, String, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add an option that provides the user with an executable file name and provides assistance with finding the location of it.
addFeedbackAction(String, SimpleListener) - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame
addFeedbackAction(String, String, SimpleListener) - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame
addFeedbackAction(String, SimpleListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback
addFeedbackAction(String, String, SimpleListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback
addField(String, String, String) - Method in class com.biomatters.geneious.publicapi.documents.DocumentHistoryEntry: Adds a DocumentHistoryEntryField to this entry
addFileSelectionOption(String, String, String, String[], String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add an option that provides functionality to let the user choose a file.
addFileSelectionOption(String, String, String, String[], String, FilenameFilter) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add an option that provides functionality to let the user choose a file.
addFileSelectionOption(String, String, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add an option that provides functionality to let the user choose a file.
addGap() - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Add an empty component which will introduce a space between the last and next component.
addGeneiousServiceListener(GeneiousServiceListener) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Add a listener to be notified about changes to this service.
addGeneratedDocument(AnnotatedPluginDocument, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Adds a newly generated document that will appear in the users local database.
addGeneratedDocuments(List<AnnotatedPluginDocument>, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Adds newly generated documents that will appear in the users local database.
addGeneratedDocuments(List<AnnotatedPluginDocument>, boolean, List<AnnotatedPluginDocument>) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Adds a list of documents that have just been generated to Geneious so that appear in the users local database and so that they become visible in the document table.
addGeneratedDocuments(List<AnnotatedPluginDocument>, boolean, List<AnnotatedPluginDocument>, WritableDatabaseService) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Adds a list of documents that have just been generated to Geneious so that appear in the users local database and so that they become visible in the document table.
addGeneratedPluginDocument(PluginDocument, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Adds a newly generated document that will appear in the users local database.
addGeneratedPluginDocuments(List<PluginDocument>, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Adds newly generated documents that will appear in the users local database.
addHelpButton(String, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Equivalent to Options.addHelpButtonOption(String, String)
addHelpButtonOption(String, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Adds a little help button (with a question mark on it) which when clicked shows a dialog containing a message
addHiddenElement(Element, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Adds a new hidden element to this database and generates a new unique name which is returned.
addHiddenElement(String, Element, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: adds a new hidden element to this database using the given name.
addHistoryEntry(DocumentHistoryEntry) - Method in class com.biomatters.geneious.publicapi.documents.DocumentHistory: See addHistoryEntry(entry, false)
addHistoryEntry(DocumentHistoryEntry, boolean) - Method in class com.biomatters.geneious.publicapi.documents.DocumentHistory: Adds a DocumentHistoryEntry to the history of this document.
addIntegerOption(String, String, Integer, Integer, Integer) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add option that stores an Integer and is displayed graphically to the user as a single line text field with a spinner (up and down arrow) on the right-hand side
For information on what the initial value of this option is set to see addStringOption.
addIntegerOption(String, String, Integer) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add option that stores an Integer and is displayed graphically to the user as a single line text field with a spinner (up and down arrow) on the right-hand side
For information on what the initial value of this option is set to see addStringOption.
addInterval(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Add one left to right interval to this annotation.
addInterval(int, int, SequenceAnnotationInterval.Direction) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Add one interval to this annotation.
addInterval(SequenceAnnotationInterval) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: add a new interval to this annotation.
addIntervals(Collection<SequenceAnnotationInterval>) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: adds a collection of intervals to this annotation
addItem(Object) - Method in class com.biomatters.geneious.publicapi.components.GComboBox
AdditionalSearchContent - Interface in com.biomatters.geneious.publicapi.documents: Interface implemented by a document which has text stored in places other than the document fields and want that text available for search.
AdditionalSearchContent.Result - Class in com.biomatters.geneious.publicapi.documents: Searchable content for a single category.
AdditionalSearchContent.Result(DocumentField, String) - Constructor for class com.biomatters.geneious.publicapi.documents.AdditionalSearchContent.Result: Constructor.
AdditionalSearchContent.Utilities - Class in com.biomatters.geneious.publicapi.documents: Small helpers for extracting searchable content from XML data.
AdditionalSearchContent.Utilities() - Constructor for class com.biomatters.geneious.publicapi.documents.AdditionalSearchContent.Utilities
AdditionalSearchContent.Utilities.Filter - Enum in com.biomatters.geneious.publicapi.documents: Various filterng options on element text.
AdditionalSearchContent.Utilities.FilterElement - Interface in com.biomatters.geneious.publicapi.documents: Provide directions on how to handle element
additionalXmlChanged() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Notifies the document that additional XML retrieved already may have changed.
addKeyStrokesToTooltips(KeyStroke, KeyStroke, KeyStroke, KeyStroke, KeyStroke) - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: Add a textual representation of a shortcut key to the tooltip for each button.
addLabel(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add a new label that is displayed between options when the options are graphically presented to the user.
addLabel(String, boolean, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add a new label that is displayed between options when the options are graphically presented to the user.
addLabelWithIcon(String, Icons) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Adds a label with an icon to the left of it.
addLicenseTypeChangeListener(SimpleListener) - Static method in class com.biomatters.geneious.publicapi.plugin.License: Adds a listener to be notified when the license changes.
addLocationChangedListener(OperationLocationOptions.LocationChangedListener) - Method in class com.biomatters.geneious.publicapi.plugin.OperationLocationOptions: Registers a listener that will be notified when the location changes.
addMultipleLineStringOption(String, String, String, int, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add an option that stores a String and is displayed to the user as a multiple line text area
It will have its value set to its default value.
addMultipleOptions(String, Options, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Adds a set of Options so that the user is able to choose to have one or more instances of these child options through the use of +/- buttons to the right of the options.
addName(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence.Builder: Adds a name that will later be used in a call to create a sequence.
addNameOfSequence(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Adds the name of a sequence that will be later added using SequenceListOnDisk.Builder.addSequence(SequenceDocument, jebl.util.ProgressListener).
addNucleotideSequence(AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: Adds a nucleotide sequence to this list that is wrapped inside an AnnotatedPluginDocument.
addNucleotideSequence(NucleotideSequenceDocument) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
addNucleotideSequence(NucleotideSequenceDocument) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceListDocument: Adds the given nucleotide sequence to the end of the list of nucleotide sequences in this document
Note that using this method will require loading the entire sequence list into memory, which might not be possible on large sequence lists.
addNucleotideSequenceNameOnFirstPass(String) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.ImportCallback: To improve import performance on nextgen sized sequence lists, an importer may optionally make a first pass of the nucleotide sequences and call this method with each sequence name during the first pass.
addOutputDocument(URN) - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument: adds an output document that this operation produced.
addOverlayIcons(Icons) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: add an icon which will be drawn on top of the standard database icon
addPluginChangedListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: Adds a listener to be notified when this plugin changes any of the functionality (services, operations, importers etc) that it provides.
addPopupEditMenu(JTextComponent) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Add a popup menu to a JTextComponent which contains the standard Edit menu actions Cut, Copy, Paste, Select All, Undo and Redo.
addPossibleValue(ValueType) - Method in class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption: Add a new value for this option.
addPrimerSelectionOption(String, String, DocumentSelectionOption.FolderOrDocuments, boolean, List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.plugin.Options: A convenience method for adding a document selection option for primers.
addProgressListener(ProgressListener) - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame: Adds a listener to be notified about all progress messages (i.e all methods in ProgressListener) that this ProgressFrame receives.
addQualifier(String, String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Add a qualifier with the specified name-value mapping.
addQualifier(SequenceAnnotationQualifier) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: add a new qualifier.
addQualifier(SequenceAnnotationQualifier) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Adds a new qualifier to this track.
addQualifiers(Collection<SequenceAnnotationQualifier>) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Adds all the given qualifiers to this annotation
addRadioOption(String, String, T[], T, Options.Alignment) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Construct a new Radio option.
addRadioOption(String, String, List<T>, T, Options.Alignment) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Construct a new Radio option.
addReferencedDocument(AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.documents.DocumentCollection: Adds the given document to a list of documents to be referenced.
addReferencedDocumentUrn(URN) - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: Adds the given document URN to a list of documents to be referenced.
addResidueAdjustment(SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Adds a residue insertion, deletion or adjustment to be applied to the sequence.
addSearchCancelledListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: Add a listener to be notified when a search on this database has been cancelled
addSearchResultPropertiesAdjuster(WritableDatabaseService.SearchResultPropertiesAdjuster) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Add a SearchResultPropertiesAdjuster to this database service.
addSelectedAnnotationsChangedListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Adds a listener to be notified when the annotations returned from SequenceViewerExtension.PropertyRetrieverAndEditor.getSelectedAnnotations() change.
addSequence(SequenceDocument) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Add a sequence to the end of the alignment.
addSequence(SequenceDocument, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Adds a new unpaired sequence.
addSequence(SequenceDocument) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Adds a new sequence for this summary.
addSequence(SequenceDocument) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
addSequence(SequenceDocument) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
addSequence(SequenceCharSequence) - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager.Builder: Adds a new sequence to this builder
addSequence() - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Adds a sequence to be managed by this paired read manager.
addSequence(SequenceDocument) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
addSequenceAnnotation(SequenceAnnotation) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Add a sequence annotation to this document.
addSequenceAnnotation(SequenceAnnotation) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument
addSequenceTrackToAdd(SequenceTrack) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Adds a new sequence track to be added to the sequence once this annotation generator finishes.
addSequenceWithMate(SequenceDocument, SequenceDocument, int, int, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Similar to addSequence but this version adds 2 sequences which are paired
addSequenceWithMate(int, int) - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager.Builder: Records the mateIndex and expected distance to the mate for the current sequence in the alignment or list.
addSequenceWithoutMate() - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager.Builder: Adds a new sequence which doesn't have a mate in this data set.
addServiceOption(String, String, WritableDatabaseService) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add an option that allows the user to select a WtiableDatabaseService which appears under one of the services returned from PluginUtilities.getWritableDatabaseServiceRoots().
addShortcutChangeListener(GeneiousActionOptions.ShortcutChangeListener) - Static method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Add a listener which will be notified whenever GeneiousActionOptions.setOverrideShortcut(javax.swing.KeyStroke) is called on a GeneiousActionOptions.
addSpanningComponent(JComponent) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Add a component which fills the entire width of the panel.
addSpanningComponent(JComponent, boolean, int) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Add a component which spans both the label and component areas.
addSpanningComponent(JComponent, boolean, int, double) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Add a component which spans both the label and component areas.
addStateChangeListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.components.MoreOptionsButton: Add a listener to the button which is fired when its state is changed between "More Options" and "Fewer Options".
addStreamHandler(String, URLStreamHandler) - Static method in class com.biomatters.geneious.publicapi.plugin.URLStreamHandlerManager: Deprecated.
Do not call
addStringOption(String, String, String, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Add an option that stores a String that is displayed graphically to the user as a single line text field.
addStringOption(String, String, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Same as addStringOption(name,label,defaultValue,null).
addSubMenuActionsChangedListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction.SubMenu: Add a simple listener to this action which will be fired when the actions in the submenu/popup-menu are changed.
addSubmenuDivider(double) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Call this on parentOptions passed into GeneiousActionOptions.createSubmenuActionOptions(GeneiousActionOptions, GeneiousActionOptions) to add a divider to the resulting sub menu.
addTrack(SequenceTrack) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Adds a new track to this sequence.
addTreeChangedListener(TreeChangeListener) - Method in class com.biomatters.geneious.publicapi.plugin.TreeViewerExtension: Add a listener to be notified when the tree changes.
addTwoComponents(JComponent, JComponent, boolean, boolean) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Add two components, one is instead of the label on the left.
addUndoSupport(JTextComponent) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Add Undo and Redo capability to a JTextComponent.
addUnusedRead(AssemblerInput.Read, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.Assembler.Callback: Adds a read that was not assembled.
addUnusedReads(SequenceListDocument, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.Assembler.Callback: Adds a list of reads that were not assembled.
addUsedRead(AssemblerInput.Read, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.Assembler.Callback: Adds a read that was assembled.
addValue(long, long) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution: Adds a new value.
addValue(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions: Clone and add a new copy of the master options to these multiple options.
addVisibleAnnotationsChangedListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Adds a listener to be notified when the annotations returned from #getVisibleAnnotations(PropertyRetrieverAndEditor.DiscardReferencesCallback) change.
addWeakDatabaseServiceListener(DatabaseServiceListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: Like DatabaseService.addWeakDatabaseServiceListener(DatabaseServiceListener) but adds a weakly referenced listener instead.
addWeakEnabledMayHaveChangedListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.Options.OptionValue: Adds a weakly referenced listener to be notified when the enabled state of this option value may have changed.
addWeakGeneiousServiceListener(GeneiousServiceListener) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Add a weakly referenced listener to be notified about changes to this service.
addWeakLicenseTypeChangeListener(SimpleListener) - Static method in class com.biomatters.geneious.publicapi.plugin.License: This method is identical to License.addLicenseTypeChangeListener(org.virion.jam.util.SimpleListener) except that only a WeakReference is stored to the listener so that it can be garbage collected when nothing else besides this class refers to it.
addWeakReferenceDocumentListener(DocumentListener) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Add a listener to be notified when the document changes.
addWeightedGap(double) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Add a gap that takes up aany additional vertical space available.
addWritableDatabaseServiceRootListener(PluginUtilities.WritableDatabaseServicesListener) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Add a listener to be notificed when root WritableDatabaseServices are added or removed.
addZoomToSelectionActionListener(ActionListener) - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: Add an actionListener to the zoom to selection button.
adjustAnnotationsForGapInsertion(List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Creates a new list of annotations by adjusting their locations to compensate for adding gaps into the sequence.
adjustAnnotationsForGapRemoval(CharSequence, List<SequenceAnnotation>) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Creates a new list of annotations by adjusting their locations to compensate for removing all the gaps in the sequence.
adjustAnnotationsForGapRemoval(List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Creates a new list of annotations by adjusting their locations to compensate for removing all the gaps in the sequence.
adjustAnnotationsForGaps(CharSequence, List<SequenceAnnotation>) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Creates a new list of annotations by adjusting their locations to compensate for adding gaps into the sequence.
adjustIntervalForGapInsertion(SequenceGapInformation) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Creates a new interval adjusted to compensate for inserting gaps into the sequence covered by this interval.
adjustIntervalForGapRemoval(SequenceGapInformation) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Creates a new interval adjusted to compensate for removing gaps from the sequence covered by this interval.
adjustProperties(AnnotatedPluginDocument, Map<String, Object>) - Method in interface com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService.SearchResultPropertiesAdjuster: Adjust the contents of searchResultProperties based on the given document.
adjustPropertyFields(List<DocumentField>) - Method in interface com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService.SearchResultPropertiesAdjuster: Adjust the contents of searchResultPropertyFields.
AdvancedSearchQueryTerm - Interface in com.biomatters.geneious.publicapi.databaseservice: Basic term in a Geneious advanced search query.
align(SequenceDocument.Alphabet, List<CharSequence>, Options, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation: Align the given sequences
ALIGN_ASSEMBLE_MENU_ACTION_OPTIONS - Static variable in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: ActionOptions for the Align/Assemble menu.
ALIGNMENT_MATCH_REGIONS_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The regions in the original sequences that the local alignment matched on
ALIGNMENT_METHOD_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The method/algorithm used to build an alignment.
ALIGNMENT_OPTIONS_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The options used to create the alignment
ALIGNMENT_PERCENTAGE_IDENTICAL - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The percentage of columns in the alignment for which all sequence are identical.
ALIGNMENT_SCORE_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The score of an alignment (the exact meaning of this depends on the particular alignment implementation)
ALIGNMENT_SIMILARITY - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The percentage of pairwise residues that are identical in the alignment, including gap versus non-gap residues, but excluding gap versus gap residues.
ALIGNMENT_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: SequenceAlignmentDocument document type
alignmentFromJeblSequences(String, List<Sequence>) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Converts the given alignment of Jebl sequences into a DefaultAlignmentDocument
AlignmentLayout - Class in com.biomatters.geneious.publicapi.documents.sequence: Provides information about how to layout of sequences (excluding the reference sequence) for rendering in an alignment or contig.
AlignmentLayout(Element) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout: Recreates an AlignmentLayout from XML.
AlignmentOperation - Class in com.biomatters.geneious.publicapi.plugin: A convenience class to enable plugins to contain alignment operations which do not need to concern themselves with: The type of documents that have been selected (sequence documents, sequence list documents, or alignment documents) Reordering and reversing of the sequences Whether the alignment is local or global Referenced documents Bases/residues unsupported by the underlying algorithm If a plugin wants to handle these itself, it could implement itself as a DocumentOperation instead, but that is not recommended.
AlignmentOperation() - Constructor for class com.biomatters.geneious.publicapi.plugin.AlignmentOperation
AlignmentOperation.InputProperties - Class in com.biomatters.geneious.publicapi.plugin: Represents the properties of the input to an AlignmentOperation
AlignmentOperation.InputProperties(OperationLocationOptions, SequenceDocument.Alphabet, boolean, boolean) - Constructor for class com.biomatters.geneious.publicapi.plugin.AlignmentOperation.InputProperties: Constructs new InputProperties.
ALL - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: A DocumentField representing an option to search all fields.
ALL_STANDARD_FIELDS - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: A list of all standard DocumentFields defined either in this class or other public API locations that are displayable to the user.
allowChangingFolderProperties() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Are the properties of this folder allowed to be changed ( moving, renaming, deleting)
ALT_KEY_STRING - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: System-dependent string used to represent the ALT key
alterSaturation(Image, double) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities: Adjust the saturation of an image.
AMBIGUITIES - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The number of untrimmed amibguity bases or residues in a chromatogram.
AMINO_ACID_SEQUENCE_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: AminoAcidSequenceDocument document type
AminoAcidSequenceDocument - Interface in com.biomatters.geneious.publicapi.documents.sequence: An interface for an Amino Acid sequence.
AnnotatedPluginDocument - Class in com.biomatters.geneious.publicapi.documents: An AnnotatedPluginDocument is a wrapper document that wraps any PluginDocument (such as a SequenceDocument or SequenceAlignmentDocument or TreeDocument) and adds extra information and provides extra functionality that the underlying PluginDocument need not concern itself with, such as allowing the user to rename the document or edit any fields displayed in the document table.
AnnotatedPluginDocument() - Constructor for class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument
AnnotatedPluginDocument.ActiveLinkSaveBehaviour - Enum in com.biomatters.geneious.publicapi.documents: Gives an action to take when AnnotatedPluginDocument.saveDocument(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.ActiveLinkSaveBehaviour, jebl.util.ProgressListener) is called.
AnnotatedPluginDocument.DocumentNotes - Interface in com.biomatters.geneious.publicapi.documents: Provides access to all the DocumentNotes on an AnnotatedPluginDocument
ANNOTATION_TYPES_NEVER_ON_TRACKS - Static variable in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: A list of annotation types that must not be places on sequence tracks.
annotationsFromXML(Element) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Return a List of SequenceAnnotations from a JDOM XML Element.
applyDisplayableOptions(T) - Method in class com.biomatters.geneious.publicapi.plugin.PluginPreferences: Applies the values of some options previously returned from PluginPreferences.getDisplayableOptions() so that these option values will be used in future calls to PluginPreferences.getActiveOptions().
applySetupOptions(Options, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService: Apply and save the specified setup options to the service.
applyToAll - Variable in class com.biomatters.geneious.publicapi.components.Dialogs.Result: True if the user checked the "Apply to all" checkbox.
areAllTreesWritable() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument: True if the tree viewer should allow the user to modify all trees in this document (if false, only the first tree will be writable)
arePermissibleExtensionsCaseSensitive() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter: Specifies whether the extensions returned by getPermissibleExtensions() should be regarded case sensitive.
areValuesGoodEnoughToContinue() - Method in class com.biomatters.geneious.publicapi.plugin.Options: This is called by Geneious when the user clicks OK in the options dialog.
ARTICLE_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: JournalArticleDocument document type
asDna() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Creates a new sequence that is identical to this sequence except with U replaced with T
asDna() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
asDna(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Views an underlying (nucleotide) CharSequence as DNA by dynamically translating 'U's to 'T's and 'u's to 't's It is guaranteed that if charSequence instanceof SequenceCharSequence, the returned value will also be instanceof SequenceCharSequence (but it may not support log-time modifications).
asInterval() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Returns this SequenceAnnotationInterval as an Interval, which uses 0-based exclusive max co-ordinates rather than 1-based inclusive max co-ordinates used by SequenceAnnotationInterval
asJeblAlignment(boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Get alignment as a Jebl alignment.
asJeblAlignment(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
asJeblAlignment(List<SequenceDocument>) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Convert a list of (aligned) Geneious sequences to a jebl alignmnent
asJeblAlignmentIfMemoryAllows(boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: This method calls #asJeblAlignment(boolean) and re-throws any OutOfMemoryError as a DocumentOperationException
asJeblSequence(SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Convert from a Geneious sequence to a jebl sequence.
asJeblSequence(SequenceAlignmentDocument.ReferencedSequence, SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Convert from a Geneious sequence to a jebl sequence.
asJeblSequence(AnnotatedPluginDocument, SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Deprecated.
use SequenceUtilities.asJeblSequence(SequenceAlignmentDocument.ReferencedSequence, SequenceDocument)
asJeblSequences(List<SequenceDocument>) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Convert a set of Geneious sequences to jebl sequences.
asJeblSequences(SequenceDocument...) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Convert a set of Geneious sequences to jebl sequences.
asLowerCase(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities: A lowercase view of the specified underlying CharSequence, i.e.
asMenuItem() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Create a JComponent for this action which can be added to a JMenu.
asRna() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Creates a new sequence that is identical to this sequence except with T replaced with U
asRna() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
asRna(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Views an underlying (nucleotide) CharSequence as RNA by dynamically translating 'T's to 'U's and 't's to 'u's It is guaranteed that if charSequence instanceof SequenceCharSequence, the returned value will also be instanceof SequenceCharSequence (but it may not support log-time modifications).
assemble(Options, AssemblerInput, ProgressListener, Assembler.Callback) - Method in class com.biomatters.geneious.publicapi.plugin.Assembler: Called to actually perform the assembly.
Assembler - Class in com.biomatters.geneious.publicapi.plugin: Allows the implementation of a read mapper, reference assembler or de novo assembler.
Assembler() - Constructor for class com.biomatters.geneious.publicapi.plugin.Assembler
Assembler.Callback - Class in com.biomatters.geneious.publicapi.plugin: Used for assembly algorithms to provide results back to Geneious.
Assembler.Callback() - Constructor for class com.biomatters.geneious.publicapi.plugin.Assembler.Callback
Assembler.ContigOutputSupport - Enum in com.biomatters.geneious.publicapi.plugin: Used for indicating whether an assembly algorithm outputs contigs, consensus sequences, or both.
Assembler.ReferenceSequenceSupport - Enum in com.biomatters.geneious.publicapi.plugin: Used for indicating whether an assembly algorithm supports no reference sequence, a single reference sequence, or multiple reference sequences.
AssemblerInput - Class in com.biomatters.geneious.publicapi.plugin: Represents the input to an assembly algorithm.
AssemblerInput(List<AnnotatedPluginDocument>, List<AssemblerInput.ReferenceSequence>, boolean) - Constructor for class com.biomatters.geneious.publicapi.plugin.AssemblerInput: Constructs some assembly input from documents that need not be loaded into memory.
AssemblerInput(List<AnnotatedPluginDocument>, List<AssemblerInput.ReferenceSequence>, boolean, double) - Constructor for class com.biomatters.geneious.publicapi.plugin.AssemblerInput: Constructs some assembly input from documents that need not be loaded into memory.
AssemblerInput(List<NucleotideSequenceDocument>, List<NucleotideSequenceDocument>, List<SequenceAlignmentDocument.ReferencedSequence>) - Constructor for class com.biomatters.geneious.publicapi.plugin.AssemblerInput: Constructs some assembly input from sequences that are all in memory.
AssemblerInput(List<NucleotideSequenceDocument>, SequenceListDocument) - Constructor for class com.biomatters.geneious.publicapi.plugin.AssemblerInput: Constructs some assembly input from sequences that are all in memory.
AssemblerInput.DataType - Enum in com.biomatters.geneious.publicapi.plugin: The sequencing technology that a sequencing read was generated from.
AssemblerInput.Properties - Class in com.biomatters.geneious.publicapi.plugin: Some properties that briefly summarise what the input will look like.
AssemblerInput.Properties(long) - Constructor for class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties
AssemblerInput.Read - Class in com.biomatters.geneious.publicapi.plugin: Represents a single read or input contig.
AssemblerInput.Read(SequenceAlignmentDocument, int) - Constructor for class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Constructs a new read consisting of a single contig.
AssemblerInput.Read(NucleotideSequenceDocument, SequenceAlignmentDocument.ReferencedSequence) - Constructor for class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Constructs a new read consisting of a single unpaired sequence.
AssemblerInput.Read(NucleotideSequenceDocument, AnnotatedPluginDocument, int) - Constructor for class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Constructs a new read consisting of a single unpaired sequence.
AssemblerInput.Read(NucleotideSequenceDocument, NucleotideSequenceDocument, int, int, SequenceAlignmentDocument.ReferencedSequence, SequenceAlignmentDocument.ReferencedSequence) - Constructor for class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Constructs a read consisting of a pair of sequences.
AssemblerInput.Read(NucleotideSequenceDocument, NucleotideSequenceDocument, int, int, AnnotatedPluginDocument, int, AnnotatedPluginDocument, int) - Constructor for class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Constructs a read consisting of a pair of sequences.
AssemblerInput.Reads - Class in com.biomatters.geneious.publicapi.plugin: Provides the ability to iterate over all reads to be assembled.
AssemblerInput.ReferenceSequence - Class in com.biomatters.geneious.publicapi.plugin: Represents a reference sequence in an assembly.
AssemblerInput.ReferenceSequence(AnnotatedPluginDocument, int) - Constructor for class com.biomatters.geneious.publicapi.plugin.AssemblerInput.ReferenceSequence: Constructs a reference sequence.
assigner - Variable in class com.biomatters.geneious.publicapi.documents.URN: Name of organization assigning names for this URN.
ASSOCIATED_OPTION_PROPERTY - Static variable in class com.biomatters.geneious.publicapi.plugin.Options: The Components (or sub-components) returned by Options.Option.getComponent() may provide this property via JComponent.getClientProperty(Object) which will be a reference to the Option the component belongs to.
asToolbarButton() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Create an AbstractButton for this action which can be added to a Toolbar.
asTranslation(CharSequence, GeneticCode) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Deprecated.
use SequenceUtilities.asTranslation(CharSequence, jebl.evolution.sequences.GeneticCode, boolean) instead.
asTranslation(CharSequence, GeneticCode, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Views an underlying (nucleotide) CharSequence as its translation.
asUpperCase(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities: Constructs an uppercase view on the specified underlying CharSequence, i.e.
attemptClose(Closeable) - Static method in class com.biomatters.geneious.publicapi.utilities.GeneralUtilities: Attempts to close a closeable, ignoring any failures (useful e.g.
Author - Class in com.biomatters.geneious.publicapi.documents: A class holding one author name.
Author() - Constructor for class com.biomatters.geneious.publicapi.documents.Author: Constructs an author with no properties
Author(String, String, String) - Constructor for class com.biomatters.geneious.publicapi.documents.Author: Constructs an author with first name, initials and surname.

B

Base64Coder - Class in com.biomatters.geneious.publicapi.utilities: A Base64 Encoder/Decoder.
Base64Coder() - Constructor for class com.biomatters.geneious.publicapi.utilities.Base64Coder
BasicSearchQuery - Interface in com.biomatters.geneious.publicapi.databaseservice: A simple, text only search query.
batchProcess(List<T>) - Method in class com.biomatters.geneious.publicapi.utilities.MultiThreadedProcessingSystem: Processes multiple values in a single thread.
batchSequenceSearch(List<AnnotatedPluginDocument>, String, Options, RetrieveCallback) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: If this is a Sequence Database (ie.
beginAlignHorizontally(String, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Starts a row of horizontally aligned options that will later be finished with a call to Options.endAlignHorizontally().
beginBorderedGroup(String, boolean) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Subsequent components will be added inside a bordered sub panel.
beginSubTask() - Method in class com.biomatters.geneious.publicapi.databaseservice.CompositeRetrieveCallback: begin a new subtask.
beginSubTask(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.CompositeRetrieveCallback: Convenience method to start the next task AND set a new message.
between(int, int) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Creates a zero-length SequenceAnnotationInterval between the given bases/residues with direction SequenceAnnotationInterval.Direction.none
BIN - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Each chromatogram or alignment is assigned to a "Low", "Medium" or "High" quality bin based on its properties.
BIN_REASON - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Each chromatogram or alignment is assigned to a "Low", "Medium" or "High" quality bin based on its properties.
BINDING_REGION_ANNOTATION_NAME - Static variable in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: The name of the annotation returned from OligoSequenceDocument.getPrimerAnnotation()
BINNING_FRAME - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The translation frame and direction which gives the least number of stop codons in the consensus sequence of a contig.
BINNING_GENETIC_CODE - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The genetic code which produces the least number of stop codons in the consensus sequence of a contig.
borderColor - Static variable in class com.biomatters.geneious.publicapi.components.OptionsPanel.RoundedLineBorder: The color of the lines on a RoundedLineBorder.
browsableContentsChanged() - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceListener: Gets called when the browse contents of this Database Service have been changed.
BubbleToolTip - Class in com.biomatters.geneious.publicapi.components: A tooltip component in the shape of a speech bubble (a rectangle on Mac because they ruin it by painting a rectangular shadow around everything).
BubbleToolTip(String, JComponent) - Constructor for class com.biomatters.geneious.publicapi.components.BubbleToolTip: A tooltip component in the shape of a speech bubble (a rectangle on Mac because they ruin it by painting a rectangular shadow around everything).
BubbleToolTip(String, JComponent, Icons) - Constructor for class com.biomatters.geneious.publicapi.components.BubbleToolTip: A tooltip component in the shape of a speech bubble (a rectangle on Mac because they ruin it by painting a rectangular shadow around everything).
build(InputStream, long) - Method in class com.biomatters.geneious.publicapi.utilities.xml.FastSaxBuilder: This builds a document from the supplied input stream.
build(Reader, long) - Method in class com.biomatters.geneious.publicapi.utilities.xml.FastSaxBuilder: This builds a document from the supplied reader
build(File) - Method in class com.biomatters.geneious.publicapi.utilities.xml.FastSaxBuilder
button - Variable in class com.biomatters.geneious.publicapi.components.Dialogs.Result: The button clicked by the user (either a String or Dialogs.DialogAction).
byteArrayFromXML(Element) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: Converts some xml created from a preious call to SequencePropertiesStorage.byteArrayToXML(String, byte[]) (String, int[])} back to a byte array.
byteArrayToXML(String, byte[]) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: Converts a byte array to xml, storing them in a compact way if possible.
ByteBackedCharSequence - Class in com.biomatters.geneious.publicapi.documents.sequence: A CharSequence whose data is stored as bytes (instead of a String) to reduce memory usage.
ByteBackedCharSequence(byte[]) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.ByteBackedCharSequence: Creates a new ByteBackedCharSequence based on the given char sequence which stores the given byte array as its internal byte array.
ByteBackedCharSequence(CharSequence) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.ByteBackedCharSequence: Constructs a new ByteBackedCharSequence based on the given char sequence
ByteBackedCharSequence(char[]) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.ByteBackedCharSequence: Constructs a new ByteBackedCharSequence based on the given char sequence
bytesToString(long) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Format a byte count to be human friendly.

C

cacheSequencesInMemory(ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk: Loads all sequences in this list into memory so that they can be quickly retrieved later using AbstractList.get(int)
calculateScore(Scores, CharSequence[], double, double, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Calculates the score for a given pairwise alignment.
CallSoon - Class in com.biomatters.geneious.publicapi.utilities: Provides a system for invoking a Runnable shortly in the Swing thread with optional coalescing of multiple calls and an optional delay until the runnable is invoked.
CallSoon() - Constructor for class com.biomatters.geneious.publicapi.utilities.CallSoon
CallSoon.EnabledProvider - Interface in com.biomatters.geneious.publicapi.utilities: Provides a method for specifying whether something is enabled
canAddAndRemoveSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Check if this alignment supports adding and removing sequences.
canAddAndRemoveSequences() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
canAddAndRemoveSequences() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
canAddAndRemoveSequences() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
CANCEL - Static variable in class com.biomatters.geneious.publicapi.components.Dialogs: An action with "Cancel" as its label.
cancel() - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame: Cancels this progress frame.
cancel(Runnable) - Static method in class com.biomatters.geneious.publicapi.utilities.CallSoon: Cancels a pending runnable (added via one of the methods if it has not yet been invoked
canDeleteDocuments(List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.databaseservice.PartiallyWritableDatabaseService: Return true if it is possible to delete all the documents in the list.
canEditDocumentField(AnnotatedPluginDocument, DocumentField) - Method in class com.biomatters.geneious.publicapi.databaseservice.PartiallyWritableDatabaseService: Returns true if it is possible to edit the given document field for the given document.
canExport(ExportableDocument.Format) - Method in interface com.biomatters.geneious.publicapi.documents.ExportableDocument: Check if a format is supported by document.
canExport(ExportableDocument.Format) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
canExport(ExportableDocument.Format) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
canExport(ExportableDocument.Format) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
canFindAll() - Method in class com.biomatters.geneious.publicapi.plugin.Findable: Returns true if this Findable supports doing a "Find All" search.
canMoveTo(WritableDatabaseService) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Can this entire database folder be moved to this new location? The default implementation always returns false.
canRemoveChildFolder(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Can the child folder with this name be removed.
canRestoreDefaults() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Return true if calling Options.restoreDefaults() would change anything.
canResume() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback
canResume() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback.Wrapper
canRunOnGeneiousServer() - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation: Returns true if this operation supports being run on a GeneiousServer.
canRunOnGeneiousServer() - Method in class com.biomatters.geneious.publicapi.plugin.Assembler: Returns true if this operation supports being run on a GeneiousServer.
canRunOnGeneiousServer() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: Returns true if this operation supports being run on a GeneiousServer.
canRunOnGeneiousServer() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
canRunOnLocalGeneious() - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation
canRunOnLocalGeneious() - Method in class com.biomatters.geneious.publicapi.plugin.Assembler: Determine whether this assembly algorithm supports being run on the current computer.
canRunOnLocalGeneious() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation
canRunOnLocalGeneious() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
canRunOnLocalGeneious() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation
canSetAnnotations() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Returns true if this alignment can have its annotations on sequences (including the consensus sequence) edited alone via SequenceAlignmentDocument.setAnnotations(int, java.util.List, boolean) and SequenceAlignmentDocument.setAnnotationsOnConsensus(java.util.List) Note that some alignment implementations may return true from SequenceAlignmentDocument.isEditable() and allow updating their annotations via SequenceAlignmentDocument.updateSequence(int, CharSequence, java.util.List, NucleotideGraph, boolean) even if they return false from this method.
canSetAnnotations() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
canSetAnnotations() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
canSetAnnotationsOnConsensus() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument
canSetAnnotationsOnConsensus() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
canSetAnnotationsOnConsensus() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
canSetFieldValue(int, DocumentField) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Returns true if this alignment supports updating field values using SequenceAlignmentDocument.setFieldValue(int, com.biomatters.geneious.publicapi.documents.DocumentField, Object, boolean)
canSetFieldValue(int, DocumentField) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
canSetSequenceNames() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Specifies whether this alignment supports changing the sequence names.
canSetSequenceNames() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
canSetSequenceNames() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
canShutdown() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: This is called to check whether the system can close.
CASE_SENSITIVE_ORDER - Static variable in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities: A Comparator that lexicographically orders CharSequences.
CENTER - Static variable in class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption
changeReferencedDocumentURNs(Map<URN, URN>) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Changes the URNs of any documents that the internal PluginDocument references.
charAt(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ByteBackedCharSequence
charAt(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Returns the char value at the specified index.
charAtIgnoringEndGaps(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Gets the character at the given index, ignoring end gaps.
CharSequenceUtilities - Class in com.biomatters.geneious.publicapi.utilities: Provides static utility methods for creating and manipulating CharSequences (not necessarily Strings).
CheckboxSearchOption - Class in com.biomatters.geneious.publicapi.databaseservice: A boolean extended search option, displayed as a check-box.
CheckboxSearchOption(String, String, boolean) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.CheckboxSearchOption: Constructor with all properties.
checkChromatogramValidity(NucleotideGraphSequenceDocument) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence: Confirms the chromatogram data is valid.
childServiceAdded(GeneiousService) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousServiceListener: Called to install a new sub/child service.
childServiceRemoved(GeneiousService) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousServiceListener: Called to remove a previously installed sub/child service.
ChromatogramDocument - Interface in com.biomatters.geneious.publicapi.documents.sequence: Deprecated.
Check for instanceof NucleotideGraphSequenceDocument instead.
classFromXML(Element, Class<? extends T>) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: recreates an object from an XML element created from a classToXML() call.
classFromXML(Element, Class<? extends T>, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: recreates an object from an XML element created from a classToXML() call.
classFromXML(Element) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: A convenience method.
classFromXML(Element, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: A convenience method.
classOfDocument - Variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: Java class of document.
classToXML(String, XMLSerializable) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: converts the given object to an XML element of the given name.
classToXML(String, XMLSerializable, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: converts the given object to an XML element of the given name.
classToXML(Geneious.MajorVersion, String, XMLSerializable, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: converts the given object to an XML element of the given name so that is is readable in the specified version of Geneious.
cleanup() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ExternalSort: If the calling code decides not to call ExternalSort.get() for all sequences added, then it should call this method to close and delete all temporary files.
CLEAR - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Clear color, new Color(0,0,0,0)
clear() - Method in class com.biomatters.geneious.publicapi.utilities.Intern: Clears the intenal cache of interned Objects.
clearReferencedDocumentUrns() - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: Clears the list of all referenced docments previously added using AbstractPluginDocument.addReferencedDocumentUrn(URN).
clipToRange(int, int) - Method in class com.biomatters.geneious.publicapi.utilities.Interval: Clips the ends of this interval so that it does not extend outside the range [minIndexInclusive,maxIndexExclusive).
clone(T) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Create a copy of an XMLSerializable object by serializing and then de-serializing it.
close() - Method in class com.biomatters.geneious.publicapi.utilities.OutputStreamThatCountsBytesWritten
close() - Method in class com.biomatters.geneious.publicapi.utilities.ProgressInputStream: Overrides FilterInputStream.close to close the progress monitor as well as the stream.
CmlDocument - Class in com.biomatters.geneious.publicapi.implementations.structure: A Cml molecular structure document.
CmlDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.structure.CmlDocument
COLOR - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The color of a document in the document table.
COLOR - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Qualifier name used to override the color of an individual annotation.
com.biomatters.geneious.publicapi.components - package com.biomatters.geneious.publicapi.components: Provides useful GUI (graphical user interface) components, none of which are necessary for creating a plugin, but many plugin implentations will find these components useful.
com.biomatters.geneious.publicapi.databaseservice - package com.biomatters.geneious.publicapi.databaseservice: Provides the interface and associated classes for defining a database service which is a service that appears on the left-hand side of the main Geneious window and provides the user with access to a database, for example NCBI or the local database for storing the user's documents.
com.biomatters.geneious.publicapi.documents - package com.biomatters.geneious.publicapi.documents: Provides interfaces and classes for defining documents in Geneious and related interfaces and classes for dealing with XMLSerialization.
com.biomatters.geneious.publicapi.documents.sequence - package com.biomatters.geneious.publicapi.documents.sequence: Provides interfaces specifying the types of sequence and alignment documents in Geneious, together with concrete classes used by sequence documents such as SequenceAnnotation and SequenceCharSequence.
com.biomatters.geneious.publicapi.documents.types - package com.biomatters.geneious.publicapi.documents.types: Provides interfaces specifying the types of documents available in Geneious.
com.biomatters.geneious.publicapi.implementations - package com.biomatters.geneious.publicapi.implementations: Provides implementations for many of the document interfaces defined in the package com.biomatters.geneious.publicapi.documents.types together with some utility classes for dealing with some of these document types.
com.biomatters.geneious.publicapi.implementations.sequence - package com.biomatters.geneious.publicapi.implementations.sequence: Provides SequenceDocument implementations for nucelotide, amino acid, and nucleotide graph (chromatogram) sequences.
com.biomatters.geneious.publicapi.implementations.structure - package com.biomatters.geneious.publicapi.implementations.structure: Provides MolecularStructureDocument implementations for many commonly used 3D structure documents.
com.biomatters.geneious.publicapi.plugin - package com.biomatters.geneious.publicapi.plugin: Provides the GeneiousPlugin interface and plugin related interfaces.
com.biomatters.geneious.publicapi.utilities - package com.biomatters.geneious.publicapi.utilities: Provides various utility methods and classes, none of which are necessary for creating a plugin, but many plugins implentations will find these methods useful.
com.biomatters.geneious.publicapi.utilities.xml - package com.biomatters.geneious.publicapi.utilities.xml
CombinedAlignmentAndAminoAcidSequenceDocument - Class in com.biomatters.geneious.publicapi.implementations.sequence: See documentation at CombinedAlignmentAndSequenceDocument
CombinedAlignmentAndAminoAcidSequenceDocument(AminoAcidSequenceDocument, SequenceAlignmentDocument, boolean, boolean) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndAminoAcidSequenceDocument: Constructs a new combined alignment and sequence document.
CombinedAlignmentAndAminoAcidSequenceDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndAminoAcidSequenceDocument: XML Deserialization constructor.
CombinedAlignmentAndNucleotideGraphSequenceDocument - Class in com.biomatters.geneious.publicapi.implementations.sequence: See documentation at CombinedAlignmentAndSequenceDocument
CombinedAlignmentAndNucleotideGraphSequenceDocument(NucleotideGraphSequenceDocument, SequenceAlignmentDocument, boolean, boolean) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideGraphSequenceDocument: Constructs a new combined alignment and sequence document.
CombinedAlignmentAndNucleotideGraphSequenceDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideGraphSequenceDocument: XML Deserialization constructor.
CombinedAlignmentAndNucleotideSequenceDocument - Class in com.biomatters.geneious.publicapi.implementations.sequence: See documentation at CombinedAlignmentAndSequenceDocument
CombinedAlignmentAndNucleotideSequenceDocument(NucleotideSequenceDocument, SequenceAlignmentDocument, boolean, boolean) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideSequenceDocument: Constructs a new combined alignment and sequence document.
CombinedAlignmentAndNucleotideSequenceDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideSequenceDocument: XML Deserialization constructor.
CombinedAlignmentAndSequenceDocument - Class in com.biomatters.geneious.publicapi.implementations.sequence: A wrapper to both an alignment and a stand-alone sequence that appears as a single EditableSequenceDocument.
CombinedAlignmentAndSequenceDocument(EditableSequenceDocument, SequenceAlignmentDocument, boolean, boolean) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument: Construct a new CombinedAlignmentAndSequenceDocument.
CombinedAlignmentAndSequenceDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument: XML Deserialization constructor.
ComboboxSearchOption - Class in com.biomatters.geneious.publicapi.databaseservice: A multi choice extended search option, displayed as a combo-box.
ComboboxSearchOption(String, String[], String, String) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.ComboboxSearchOption: Default constructor.
ComboboxSearchOption(String, String[], String, String, boolean) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.ComboboxSearchOption
commaFormat(long) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Formats the given number with commas every 3rd digit.
COMMAND_KEY_CHAR - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: The character used to represent the command key on Apple Macs (the "cloverleaf").
COMMON_NAME_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Visible, editable field representing the common name for the organism of a sequence.
commonPrefixLength(CharSequence, CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities: The length of the longest common (case sensitive) prefix of the two specified CharSequences a and b, i.e.
compact() - Method in class com.biomatters.geneious.publicapi.utilities.IntList.Array: Compacts the underlying storage array to only big as big as it needs to be to hold the current data.
compactAminoAcidSequences(List<AminoAcidSequenceDocument>, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Attempts to compact the memory usage of as many sequences in the given list of sequences as possible by replacing them with ImmutableSequence instances.
compactNucleotideSequences(List<NucleotideSequenceDocument>, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Attempts to compact the memory usage of as many sequences in the given list of sequences as possible by replacing them with ImmutableSequence instances.
CompactQualityOnlyGraph - Class in com.biomatters.geneious.publicapi.documents.sequence: A memory efficient nucleotide graph that only supports quality values in the range 0->256 and does not support traces.
CompactQualityOnlyGraph(byte[]) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph: Constructs a new graph.
compareTo(Object) - Method in class com.biomatters.geneious.publicapi.documents.Author
compareTo(SequenceCharSequence) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Lexicographically compares this SequenceCharSequence to another, taking into account case.
compareTo(EValue) - Method in class com.biomatters.geneious.publicapi.implementations.EValue
compareTo(Percentage) - Method in class com.biomatters.geneious.publicapi.implementations.Percentage
CompositeRetrieveCallback - Class in com.biomatters.geneious.publicapi.databaseservice: A RetrieveCallback that is suitable for a task that consists of several subtasks.
CompositeRetrieveCallback(RetrieveCallback, int) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.CompositeRetrieveCallback: Construct a CompositeProgressListener with a number of evenly weighted subtasks.
CompositeRetrieveCallback(RetrieveCallback, double...) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.CompositeRetrieveCallback: construct a new composite RetrieveCallback.
CompoundSearchQuery - Interface in com.biomatters.geneious.publicapi.databaseservice: A compound query is a set of queries combined by a logical operator.
CompoundSearchQuery.Operator - Enum in com.biomatters.geneious.publicapi.databaseservice: Ways to connect the terms of a compound query.
CompressionUtilities - Class in com.biomatters.geneious.publicapi.utilities: Provides methods for reading from compressed files.
CompressionUtilities() - Constructor for class com.biomatters.geneious.publicapi.utilities.CompressionUtilities
CompressionUtilities.CompressedFileWrapper - Class in com.biomatters.geneious.publicapi.utilities: A wrapper class for a compressed file.
CompressionUtilities.CompressionMethod - Enum in com.biomatters.geneious.publicapi.utilities: Represents a type of compression
concatenate(List<CharSequence>) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities: Creates a CharSequence that represents a concatenation of the specified CharSequences in the order in which they appear in the specified list.
ConcatenatedList<T> - Class in com.biomatters.geneious.publicapi.utilities: A list made by joining multiple sublists of Ts together.
Condition - Enum in com.biomatters.geneious.publicapi.documents: Available types of conditions.
condition - Variable in class com.biomatters.geneious.publicapi.documents.Constraint
conditions - Variable in class com.biomatters.geneious.publicapi.databaseservice.QueryField: Possible conditions on field.
confirmDocumentValid() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Confirms this document is valid.
conformsToConstraint(Object) - Method in class com.biomatters.geneious.publicapi.documents.Constraint: Returns true if value conforms to this constraint, false if not.
CONSENSUS_SEQUENCE_LENGTH - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The approximate length of the consensus sequence in a contig.
CONSENSUS_SOURCE_SEQUENCES_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The number of sequences in the contig that a consensus sequence was generated from
Constraint - Class in com.biomatters.geneious.publicapi.documents: The idea of a Constraint is very simple.
constraintsToString(Constraint[]) - Static method in class com.biomatters.geneious.publicapi.documents.Constraint: A convenient method to neatly list the Constraints.
contains(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Checks whether this interval includes the residue at the specified index.
contains(SequenceAnnotationInterval) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Determines if this interval entirely covers another interval.
contains(char) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Checks whether this CharSequence contains the specified character.
contains(CharSequence, char) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities: Checks whether a CharSequence contains the specified character.
contains(int) - Method in class com.biomatters.geneious.publicapi.utilities.Interval
contains(Interval) - Method in class com.biomatters.geneious.publicapi.utilities.Interval
contains(List<Interval>, int) - Static method in class com.biomatters.geneious.publicapi.utilities.Interval: Determine if at least one of the given intervals contains this index.
contains(int) - Method in class com.biomatters.geneious.publicapi.utilities.IntList: Returns true if this list contains this value.
containsDocumentAnywhereWithinDatabase(URN) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Determine if this database (including any other folders and any user invisible folders) contains a document with this URN This method should return the same information no matter where in the DatabaseService tree it is called.
containsInvalidResidues(SequenceType, boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: performs a quick test to see if this sequence contains possilby contains invalid residues for its sequence type.
containsInvalidResidues(SequenceDocument, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Checks if a sequence contain invalid sequence residues.
containsInvalidResidues(CharSequence, SequenceDocument.Alphabet, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Checks if a sequence contain invalid sequence residues.
containsInvalidResidues(CharSequence, SequenceType, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Checks if a sequence contain invalid sequence residues.
containsOnPotentiallyCircularSequence(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Checks whether this interval includes the residue at the specified index in a potentially circular sequence.
CONTIG_MEAN_COVERAGE - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Mean number of sequences covering a column in an assembly
All SequenceAlignmentDocuments created in 7.0 or later (or just small ones created prior to 7.0) with SequenceAlignmentDocument.isContig()==true have this field
CONTIG_PERCENTAGE_OF_REFERENCE_SEQUENCE_COVERED - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The percentage of the reference sequence in a contig that is covered by one or more reads.
CONTIG_REFERENCE_SEQUENCE_INDEX - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The index of the reference sequence in an alignment contig or -1 if there is no reference sequence.
CONTIG_REFERENCE_SEQUENCE_LENGTH - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The length of the reference sequence (if any) in an alignment or contig.
CONTIG_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: Contig document type
CONTINUE - Static variable in class com.biomatters.geneious.publicapi.components.Dialogs: An action with "Continue" as its label.
CONTINUE_CANCEL - Static variable in class com.biomatters.geneious.publicapi.components.Dialogs: Use this to specify that a dialog should have "Continue" and "Cancel" buttons.
controlPreference - Variable in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousDependentPreference: Deprecated.

The preference whos selected value determines the enabled state of the GeneiousPreferences.GeneiousDependentPreference.dependentPreferences.
convertStringToInputType(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.TextFieldSearchOption: Converts a String, e.g.
copyAllDocumentFields(SequenceDocument, DefaultSequenceDocument) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Copy all document fields (such as organism, taxonomy and common name) from any SequenceDocument to a DefaultSequenceDocument.
copyDataFrom(SequenceTrack) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Copies all data from another track into this track so that this track contains identical data to the given one.
copyDirectory(File, File, boolean, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Recursively copies the entire contents of one directory to another.
copyDocumentFields(SequenceDocument, DefaultSequenceDocument, boolean) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Copy important document fields (such as organism, taxonomy and common name) from any SequenceDocument to any DefaultSequenceDocument
copyFile(File, File, FileUtilities.TargetExistsAction, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Copies the contents of a file to another file If canceled in the middle of the copy (so that the destination file is partially written), the destination file will be deleted.
copyOf(NucleotideGraph) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Creates a copy of the given graph.
copyOf(List<SequenceAnnotation>) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Creates a deep copy of a list of SequenceAnnotations.
copySequenceTracksFrom(SequenceDocument) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Copies all SequenceTracks (if any) from the source sequence on to this sequence.
copyWithoutIntervals() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Creates a copy of this annotation, without any intervals.
CORNER_WIDTH - Static variable in class com.biomatters.geneious.publicapi.components.OptionsPanel.RoundedLineBorder: The roundedness of the corners of the border.
count(char) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Counts the number of occurences of c in this CharSequence
count(char, CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities: Counts the number of occurrences of c in charSequence
countGaps(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Counts the number of gaps in this sequence between the 2 given positions.
create(List<T>, boolean, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk: Creates a new SequenceListOnDisk from an existing list of ungapped sequences.
create() - Method in interface com.biomatters.geneious.publicapi.plugin.Options.ComponentCreator: Creates the component now.
create(List<? extends List<? extends T>>) - Static method in class com.biomatters.geneious.publicapi.utilities.ConcatenatedList: Creates a List with the given sublists May or may not be a ConcatenatedList.
create(List<? extends T>...) - Static method in class com.biomatters.geneious.publicapi.utilities.ConcatenatedList: Creates a List with the given sublists May or may not be a ConcatenatedList.
createAdvancedPanel() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Creates a graphical panel used to display advanced options.
createAndQuery(Query[], Map<String, Object>) - Static method in class com.biomatters.geneious.publicapi.databaseservice.Query.Factory: Creates an AND query
createAnnotatedPluginDocument(PluginDocument) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Equivalent to createAnnotatedPluginDocument(document,ProgressListener.EMPTY)
createAnnotatedPluginDocument(PluginDocument, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Creates an AnnotatedPluginDocument from a PluginDocument.
createAnnotatedPluginDocument(Element, ElementProvider, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Deprecated.
use DocumentUtilities.createAnnotatedPluginDocument(org.jdom.Element, ElementProvider, boolean) instead, where the final parameter of null is equivalent to assignNewURN==false or URN.generateUniqueLocalURN() for assignNewURN==true
createAnnotatedPluginDocument(Element, ElementProvider, String) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Deprecated.
use DocumentUtilities.createAnnotatedPluginDocument(org.jdom.Element, ElementProvider, URN) instead.
createAnnotatedPluginDocument(Element, ElementProvider, URN) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Creates an AnnotatedPluginDocument without the internal PluginDocument included.
createAnnotatedPluginDocuments(List<? extends PluginDocument>) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Creates a list of AnnotatedPluginDocuments from a list of PluginDocuments.
createAnnotatedPluginDocuments(PluginDocument) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: creates a list of AnnotatedPluginDocuments from a single of PluginDocument.
createBooleanField(String, String, String, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: Creates a DocumentField with a Boolean value.
createBooleanNoteField(String, String, String, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Construct a DocumentNoteField that represents a boolean (true/false) value
createBrowseQuery() - Static method in class com.biomatters.geneious.publicapi.databaseservice.Query.Factory: Creates a browse query that will return all documents in the database folder, excluding any child database folders.
createChildFolder(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Creates a child DatabaseService.
createCompactCharSequence(CharSequence) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceBuilder: Equivalent to createCompactCharSequence(charSequence, false)
createCompactCharSequence(CharSequence, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceBuilder: Creates a charSequence which uses a minimal amount of memory to represent the given charSequence by analyzing the contents and returning an appropriate CharSequence implementation.
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.BooleanOption
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.DateOption
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.EditableComboBoxOption
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.ExecutableFileSelectionOption
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleLineStringOption
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Create a graphical component representing this option.
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.RadioOption
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.StringOption
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionGrabOption
createComponent() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension
createConstraint(Class, Condition, Object) - Static method in class com.biomatters.geneious.publicapi.documents.Constraint: Construct a constraint with the given options
createContentHandler() - Method in class com.biomatters.geneious.publicapi.utilities.xml.FastSaxBuilder
createCopy() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Creates a copy of this sequence
createCopy() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Creates a copy of this sequence track.
createCopy() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
createCopyOf(SequenceDocument, boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence.Builder: Creates a ImmutableSequence copy of a given sequence.
createCopyWithNameSuffix(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Creates a new sequence identical to this once except with a different name.
createCopyWithNameSuffix(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
createCopyWithNewName(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Creates a new sequence identical to this once except with a different name.
createCopyWithNewName(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
createCopyWithoutAnnotations() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Creates a new track which is equivalent to this track, but without any of the annotations.
createCustomCursor(Icon, String, int, int) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Create a cursor from an icon.
createCustomField(String, String, String, Class<? extends XMLSerializable>) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: Creates a DocumentField with a value of arbitrary type.
createCustomField(String, String, String, Class<? extends XMLSerializable>, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: Creates a DocumentField with a value of arbitrary type.
CREATED_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Non-visible, editable field representing a document's creation date.
createDateField(String, String, String) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: Creates a DocumentField with a Date value.
createDateField(String, String, String, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: Creates a DocumentField with a Date value.
createDateNoteField(String, String, String, List<Constraint>, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Construct a DocumentNoteField that represents a date value
createDecimalNoteField(String, String, String, List<Constraint>, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Construct a DocumentNoteField that represents a decimal (real number) value
createDocumentBasedGraph(AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraphFactory: Deprecated.
This method causes ambiguity about whether the Alignment of Sequence aspect of a CombinedAlignmentAndSequenceDocument is required so is no longer used on CombinedAlignmentAndSequenceDocuments. All implementations should instead implement SequenceGraphFactory.createDocumentBasedGraphForAlignment(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument) or SequenceGraphFactory.createDocumentBasedGraphForSequence(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument).
createDocumentBasedGraphForAlignment(AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraphFactory: Create a new document based Alignment Graph.
createDocumentBasedGraphForSequence(AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraphFactory: Create a new document based SequenceGraph.
createDocumentHistoryEntry() - Method in class com.biomatters.geneious.publicapi.documents.DocumentHistory: Create a historyEntry which can then have entryFields added to it before it is passed to one of the addHistoryEntry methods in this class.
createDocumentNote() - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType: Get an instance of DocumentNote with this as its note type.
createDoubleField(String, String, String) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: Creates a DocumentField with a Double value.
createDoubleField(String, String, String, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: Creates a DocumentField with a Double value.
createEnumeratedField(String[], String, String, String, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: Creates a DocumentField with an enumerated set of possible String values.
createEnumeratedNoteField(String[], String, String, String, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Construct a DocumentNoteField that represents a String (text) value that must be from a set of predefined values.
createExtendedPrintable(JComponent) - Static method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Factory: Creates an ExtendedPrintable for a JComponent.
createExtendedQuery(String, Map<String, Object>) - Static method in class com.biomatters.geneious.publicapi.databaseservice.Query.Factory: This creates a query with extended options (stored in a map as key/value combinations)
createExtensionForPrimerAnnotation(SequenceAnnotation) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Deprecated.
this method no longer works and there is no replacement in the API. Sorry!
createFieldQuery(DocumentField, Condition, Object) - Static method in class com.biomatters.geneious.publicapi.databaseservice.Query.Factory: This creates a query to see if a given field value matches a condition.
createFieldQuery(DocumentField, Condition, Object[]) - Static method in class com.biomatters.geneious.publicapi.databaseservice.Query.Factory: This creates a query to see if a given field value matches a condition.
createFieldQuery(DocumentField, Condition, Object[], Map<String, Object>) - Static method in class com.biomatters.geneious.publicapi.databaseservice.Query.Factory: This creates a query to see if a given field value matches a condition.
createFolderViewFolder(String, AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Creates a new child folder that contains a document that may be displayed for representing an entire view of the folder.
createFromBaseElement(Element) - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: Restore document from base element.
createGapInsertingManager(PluginDocument, SequenceGapInformation, boolean, SimpleListener) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Creates a new manager that inserts gaps into annotations relative to this manager.
createGapRemovingManager(PluginDocument, SequenceGapInformation, boolean, SimpleListener) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Creates a new manager that removes gaps from annotations relative to this manager.
createGraphWithAdjustedEndGaps(ExtendedNucleotideGraph, int, int) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Creates a copy of the given graph with the length of its end gaps adjusted.
createGrayedOutIcons(Icons, double, float) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities: Creates and caches a version of the icons with less (or more) saturation and/or a change in alpha.
createHardLink(File, File) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Creates a file system hard link.
createHelpButton() - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities
createHelpButton(boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities
createHelpButton(String, String) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Creates a help style button that displays a help dialog with when clicked on
createHelpButton(boolean, String, String) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Creates a help style button that displays a help dialog with when clicked on
createHtmlPane(String) - Static method in class com.biomatters.geneious.publicapi.components.GTextPane: Create a non-editable GTextPane containing the given HTML.
createIconUrl(Icon) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities: Takes an icon and saves it to disk so then returns the path to the image file.
createImmutableSequence(SequenceDocument, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Creates an ImmutableSequence copy of another sequence.
createImmutableSequence(SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Creates an ImmutableSequence copy of another sequence if possible.
createIntegerField(String, String, String) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: Creates a DocumentField with an Integer value.
createIntegerField(String, String, String, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: Creates a DocumentField with an Integer value.
createIntegerNoteField(String, String, String, List<Constraint>, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Construct a DocumentNoteField that represents an integer (whole number) value
createInterlaced(SequenceListOnDisk<T>, SequenceListOnDisk<T>, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk: Creates a new SequenceListOnDisk by interlacing a pair of existing SequenceListOnDisks.
createIteratableForIntervalList(List<Interval>) - Static method in class com.biomatters.geneious.publicapi.utilities.Interval: Returns an Iterable that iterates over each value in each interval in a given list of intervals.
createLongField(String, String, String, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: Creates a DocumentField with a Long value.
createNewDocumentByTransformingSequences(SequenceDocument.Alphabet, SequenceDocument.Transformer, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: Equivalent to createNewDocumentByTransformingSequences(alphabet, transformer, progressListener, true).
createNewDocumentByTransformingSequences(SequenceDocument.Alphabet, SequenceDocument.Transformer, ProgressListener, boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: Creates a new DefaultSequenceListDocument (whose sequences will be a SequenceListOnDisk) by applying a transformation to each of the sequences in this list.
createNewDocumentsByTransformingSequences(List<AnnotatedPluginDocument>, SequenceDocument.Transformer, ProgressListener, String) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Transforms the sequence(s) in each input document and returns a new document corresponding to each input document.
createNewNoteType(String, String, String, List<DocumentNoteField>, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentNoteUtilities: Create a new DocumentNoteType which should be used for adding a new note type.
createNewSequenceWhenAppliedTo(SequenceDocument) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Returns the results of applying this annotation generator result to the given sequence.
createNucleotideGraph(int[][], int[], int[], int, int, int, int) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Creates a new nucleotide graph.
createNucleotideGraph(int[], int, int) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Creates a new nucleotide graph with qualities but no traces.
createNucleotideGraph(int[][], int[], int[], int, int) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Creates a new nucleotide graph.
createNucleotideGraph(NucleotideGraph) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Creates a deep copy of the given graph.
createNucleotideGraphAdjustedForGapInsertion(NucleotideGraph, CharSequence) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Creates a deep copy of the given graph with all graph values adjusted to compensate for gap insertion as indicated by the presense of gaps in charSequence.
createNucleotideGraphSequence(String, CharSequence, NucleotideGraph) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence.Builder: Creates a nucleotide graph sequence compacted to use as little memory as possible
createNucleotideGraphSequence(String, CharSequence, int[]) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence.Builder: Creates a nucleotide graph sequence compacted to use as little memory as possible
createNucleotideSequence(String, CharSequence) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence.Builder: Creates a nucleotide sequence compacted to use as little memory as possible
createOptions() - Method in class com.biomatters.geneious.publicapi.plugin.PluginPreferences: Creates a new instance of the options.
createOrQuery(Query[], Map<String, Object>) - Static method in class com.biomatters.geneious.publicapi.databaseservice.Query.Factory: Creates an OR query
createPanel() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Creates a graphical panel used to display these options.
createQuery(String) - Static method in class com.biomatters.geneious.publicapi.databaseservice.Query.Factory: Creates a query based on the provided query string.
createResidueBasedGraph(SequenceDocument.Alphabet, boolean, boolean, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraphFactory: Create a new residue based SequenceGraph for a sequence or alignment.
createSequenceAlignmentGraphFactory(String, String, boolean, int, SequenceDocument.Alphabet, DefaultSequenceGraphFactories.SingleSequenceScorer, boolean) - Static method in class com.biomatters.geneious.publicapi.implementations.DefaultSequenceGraphFactories: Create a SequenceGraphFactory that is averaged over multiple sequences from a single sequence scorer.
createSequenceAlignmentGraphFactory(String, String, boolean, int, SequenceDocument.Alphabet, DefaultSequenceGraphFactories.SequenceAlignmentScorer, boolean) - Static method in class com.biomatters.geneious.publicapi.implementations.DefaultSequenceGraphFactories: Create a SequenceGraphFactory for sequence alignments.
createSequenceCopy(SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Creates a copy of the original sequence if necessary.
createSequenceCopyAdjustedForGapInsertion(SequenceDocument, CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Creates a copy of the given sequence with annotations, sequence residues, and chromatogram values adjusted to account for gap insertion.
createSequenceCopyEditable(SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Creates a copy of the original sequence that is editable.
createSequenceDocument(SequenceType, String, String, CharSequence, Date) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Creates a DefaultNucleotideSequence or DefaultAminoAcidSequence depending on sequenceType.
createSequenceViewerExtension(DocumentViewer, AnnotatedPluginDocument[], SequenceViewerExtension.PropertyRetrieverAndEditor) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.Factory: Creates an instance of a sequence viewer extension.
createSequenceViewerExtension(DocumentViewer, AnnotatedPluginDocument[], SequenceViewerExtension.PropertyRetrieverAndEditor) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsFactory
createSingleSequenceGraphFactory(String, String, boolean, int, SequenceDocument.Alphabet, DefaultSequenceGraphFactories.SingleSequenceScorer, boolean) - Static method in class com.biomatters.geneious.publicapi.implementations.DefaultSequenceGraphFactories: Create a SequenceGraphFactory for a single sequence where graph points depend only on the residue at that point.
createStatistics(SequenceViewerExtension.PropertyRetrieverAndEditor, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsFactory: Generates one or more sections of statistics to be displayed in the statistics controls section.
createString(char[]) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Creates a new String from a character array by calling the String package private constructor: String.String(int, int, char[]) which shares the char[] value array for speed and lowers memory usage since we don't need to have 2 copies of the char[] in memory at once.
createString(int, int, char[]) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Creates a new String from a character array by calling the String package private constructor: String.String(int,int,char[]) which shares the char[] value array for speed and lowers memory usage since we don't need to have 2 copies of the char[] in memory at once.
createStringField(String, String, String, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: Creates a DocumentField with a String value, that may or may not be visible and may or may not be editable.
createStringField(String, String, String) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: Creates a DocumentField with a String value.
createSubmenuActionOptions(GeneiousActionOptions, GeneiousActionOptions) - Static method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Create options for an action which will appear in a submenu (if in a menu) or a popup button (if in the toolbar).
createTempDir(boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Creates a temporary directory.
createTempFile(String, String) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Deprecated.
use FileUtilities.createTempFile(String, String, boolean) instead.
createTempFile(String, String, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Creates a temporary file as specified by File.createTempFile(String, String, java.io.File).
createTempFile(String, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Returns a temporary file with the given name.
createTextComponentForDialog(String, boolean, Dialogs.DialogOptions) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Create a component to display a String message in a dialog.
createTextNoteField(String, String, String, List<Constraint>, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Construct a DocumentNoteField that represents a String (text) value.
createTreeViewerExtension(DocumentViewer, AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.plugin.TreeViewerExtension.Factory: Optionally create a TreeViewerExtension for a given AnnotatedPluginDocument.
createTreeViewerExtension(AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.plugin.TreeViewerExtension.Factory: Deprecated.
Use TreeViewerExtension.Factory.createTreeViewerExtension(DocumentViewer, com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument) instead.
createTrimAnnotation(int, int) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Creates a new SequenceAnnotation.TYPE_TRIMMED annotation
createURLField(String, String, String) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: Creates a DocumentField with a URL value.
createUrnForDocumentSoonToBeAdded() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Returns a URN which can be specified as used for document later added to this database using WritableDatabaseService.addDocumentCopyWithProperties(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, jebl.util.ProgressListener, java.util.Map, com.biomatters.geneious.publicapi.documents.URN).
createViewer(AnnotatedPluginDocument[]) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory: Viewer as a Java component.
CTRL_KEY_STRING - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: System-dependent string used to represent the CTRL key
currentTimeMillis() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities: Like System.currentTimeMillis() except on Windows platforms, this returns time with precision to the nearest millisecond instead of nearest 15 milliseconds which is the accuracy of System.currentTimeMillis().

D

DatabaseService - Class in com.biomatters.geneious.publicapi.databaseservice: A Geneious service providing documents in response to a search query.
DatabaseService() - Constructor for class com.biomatters.geneious.publicapi.databaseservice.DatabaseService
DatabaseService.SequenceSearchQueryType - Enum in com.biomatters.geneious.publicapi.databaseservice: The type of query for a sequence search
DatabaseServiceException - Exception in com.biomatters.geneious.publicapi.databaseservice: Most database service methods may throw this exception.
DatabaseServiceException(String, boolean) - Constructor for exception com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceException: Constructor.
DatabaseServiceException(Throwable, String, boolean) - Constructor for exception com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceException: Constructor.
DatabaseServiceListener - Class in com.biomatters.geneious.publicapi.databaseservice: Code using a DatabaseService can get notified of special events by registering this listener via addDatabaseServiceListener.
DatabaseServiceListener() - Constructor for class com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceListener
DataInputOutputUtilities - Class in com.biomatters.geneious.publicapi.utilities: Provides methods for reading and writing objects from DataInputStream and DataOutputStream
DataInputOutputUtilities() - Constructor for class com.biomatters.geneious.publicapi.utilities.DataInputOutputUtilities
DE_NOVO_UNIQUE_ID_SUFFIX - Static variable in class com.biomatters.geneious.publicapi.plugin.Assembler: If an assembly implementation supports both reference sequence and de novo assembly, its de novo assembler Assembler.getUniqueId() should end with this.
decode(char[]) - Static method in class com.biomatters.geneious.publicapi.utilities.Base64Coder: Decodes Base64 data.
DEFAULT_EXTRACTION_STRATEGY - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments: The default ExtractionStrategy used to return sequences.
DEFAULT_FOCUSED_TEXT_COMPONENT_KEY - Static variable in class com.biomatters.geneious.publicapi.components.Dialogs: By calling putClientProperty() on a JTextField with this as the key and Boolean.TRUE as the value, calling code may nominate that field to be the "first" text component, which will be initially selected when the dialog is displayed.
DEFAULT_POSITION - Static variable in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: The default menuPosition for GeneiousActionOptions.
DefaultAlignmentDocument - Class in com.biomatters.geneious.publicapi.implementations: An implementation of a SequenceAlignmentDocument.
DefaultAlignmentDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Constructs a new empty alignment.
DefaultAlignmentDocument(String, SequenceDocument...) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Constructs alignment document with no references to original sequence documents.
DefaultAlignmentDocument(SequenceDocument[], String, Double, String) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Deprecated.
use DefaultAlignmentDocument.DefaultAlignmentDocument(String, com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument...) instead.
DefaultAlignmentDocument(SequenceDocument[], AnnotatedPluginDocument[], CharSequence[], String, Double, String) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: This is the constructor that should be used in most situations.
DefaultAlignmentDocument(SequenceDocument[], CharSequence[], String, Double, String, ProgressListener) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Constructs an alignment without any references back to the original sequences.
DefaultAlignmentDocument(SequenceDocument[], List<SequenceAlignmentDocument.ReferencedSequence>, CharSequence[], String, Double, String, ProgressListener) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: This is the constructor that should be used in most situations.
DefaultAlignmentDocument(AnnotatedPluginDocument[], CharSequence[], String, Double) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Constructs an alignment with references to original sequence documents.
DefaultAlignmentDocument(SequenceAlignmentDocument) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Construct a default alignment as a deep copy of another alignment.
DefaultAminoAcidSequence - Class in com.biomatters.geneious.publicapi.implementations.sequence: A plugin document holding one amino acid sequence.
DefaultAminoAcidSequence() - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultAminoAcidSequence: empty constructor, Plugin document requirement.
DefaultAminoAcidSequence(String, CharSequence) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultAminoAcidSequence: Construct a new amino acid sequence.
DefaultAminoAcidSequence(String, String, CharSequence, Date) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultAminoAcidSequence: Construct a new amino acid sequence.
DefaultAminoAcidSequence(String, String, CharSequence, Date, URN) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultAminoAcidSequence: Construct a new amino acid sequence.
DefaultAminoAcidSequence(AminoAcidSequenceDocument, Date) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultAminoAcidSequence: Creates a new DefaultAminoAcidSequence as a copy of the specified AminoAcidSequenceDocument.
DefaultAminoAcidSequence(Sequence) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultAminoAcidSequence: Construct from a sequence in jebl format.
DefaultHyperlinkListener - Class in com.biomatters.geneious.publicapi.components: A simple implementation of HyperlinkListener which invokes the system's default browser.
DefaultHyperlinkListener() - Constructor for class com.biomatters.geneious.publicapi.components.DefaultHyperlinkListener: Construct a new DefaultHyperlinkListener
defaultLinuxViewers() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileExporterAndExternalViewer: Linux application name(s) of viewers.
DefaultMolecularStructureDocument - Class in com.biomatters.geneious.publicapi.implementations.structure: An implementation of a MolecularStructureDocument.
DefaultMolecularStructureDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.structure.DefaultMolecularStructureDocument
DefaultNucleotideGraph - Class in com.biomatters.geneious.publicapi.documents.sequence: A NucleotideGraph that stores its values in int[] arrays internally, and allows getting and setting those arrays.
DefaultNucleotideGraph(int[][], int[], int[], int, int) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Construct a new DefaultNucleotideGraph.
DefaultNucleotideGraphSequence - Class in com.biomatters.geneious.publicapi.implementations.sequence: An implementation of an editable chromatogram.
DefaultNucleotideGraphSequence() - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence: empty constructor for XML serialisation purposes
DefaultNucleotideGraphSequence(NucleotideGraphSequenceDocument, Date) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence: Create a DefaultNucleotideGraphSequence from an existing document.
DefaultNucleotideGraphSequence(String, String, CharSequence, Date, NucleotideGraph) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence: Create a DefaultNucleotideGraphSequence from any chromatogram.
DefaultNucleotideGraphSequence(String, String, CharSequence, Date, NucleotideGraph, URN) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence: Create a DefaultNucleotideGraphSequence from any chromatogram.
DefaultNucleotideSequence - Class in com.biomatters.geneious.publicapi.implementations.sequence: A plugin document holding one nucleotide sequence.
DefaultNucleotideSequence() - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideSequence: empty constructor, Plugin document requirement.
DefaultNucleotideSequence(String, CharSequence) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideSequence: Construct a new nucleotide sequence.
DefaultNucleotideSequence(String, String, CharSequence, Date) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideSequence: Construct a new nucelotide sequence.
DefaultNucleotideSequence(String, String, CharSequence, Date, URN) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideSequence: Construct a new nucelotide sequence.
DefaultNucleotideSequence(NucleotideSequenceDocument, Date) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideSequence: Constructs a DefaultNucleotideSequence as a copy of an existing NucleotideSequenceDocument.
DefaultNucleotideSequence(Sequence) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideSequence: Construct from a sequence in jebl format.
DefaultPhylogenyDocument - Class in com.biomatters.geneious.publicapi.implementations: An implementation of a Phylogeny document.
DefaultPhylogenyDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument: XML deserialization constructor.
DefaultPhylogenyDocument(Element) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument: XML deserialization constructor.
DefaultPhylogenyDocument(List<? extends Tree>, List<Sequence>, String, String, AnnotatedPluginDocument, boolean) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
DefaultPhylogenyDocument(List<? extends Tree>, List<Sequence>, String, String, AnnotatedPluginDocument, boolean, boolean) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
DefaultSameTaxaTreesDocument - Class in com.biomatters.geneious.publicapi.implementations: A default implementation of a plugin document holding a list of trees.
DefaultSameTaxaTreesDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument: XML deserialization constructor.
DefaultSameTaxaTreesDocument(List<? extends Tree>, String, Date) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument: Construct from explicit values
DefaultSameTaxaTreesDocument(Element) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument: XML deserialization constructor.
DefaultSequenceDocument - Class in com.biomatters.geneious.publicapi.implementations.sequence: A default implementation of a sequence document.
DefaultSequenceDocument(String, String, CharSequence, Date) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
DefaultSequenceDocument(String, String, CharSequence, Date, URN) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
DefaultSequenceDocument(SequenceDocument, Date) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Construct a new DefaultSequenceDocument from an existing SequenceDocument.
DefaultSequenceDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Construct a DefaultSequenceDocument with no arguments.
DefaultSequenceDocument(Sequence) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Construct a new DefaultSequenceDocument using a Sequence from JEBL.
DefaultSequenceDocument.Cache - Class in com.biomatters.geneious.publicapi.implementations.sequence: Used for controlling caching of the char sequence and annotations controlled from this class.
DefaultSequenceDocument.Cache() - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument.Cache: Constructs a new cache.
DefaultSequenceGraphFactories - Class in com.biomatters.geneious.publicapi.implementations: Provides convenience functionality to create a SequenceGraphFactory which draws a bar graph from some simpler interfaces.
DefaultSequenceGraphFactories.SequenceAlignmentScorer - Class in com.biomatters.geneious.publicapi.implementations: Provides methods to supply a score for a given set of sequence residues and provide a color for a given score.
DefaultSequenceGraphFactories.SequenceAlignmentScorer() - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultSequenceGraphFactories.SequenceAlignmentScorer
DefaultSequenceGraphFactories.SingleSequenceScorer - Class in com.biomatters.geneious.publicapi.implementations: Provides methods to supply a score for a given sequence residue and provide a color for a given score.
DefaultSequenceGraphFactories.SingleSequenceScorer() - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultSequenceGraphFactories.SingleSequenceScorer
DefaultSequenceListDocument - Class in com.biomatters.geneious.publicapi.documents.sequence: A default implementation of a SequenceListDocument.
DefaultSequenceListDocument() - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: XML deserialization constructor.
DefaultTreeDocument - Class in com.biomatters.geneious.publicapi.implementations: A default implementation of a plugin document holding a tree.
DefaultTreeDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument: XML deserialization constructor.
DefaultTreeDocument(RootedTree, String, String, Date) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument: Construct tree with explicit parameters
DefaultTreeDocument(Tree, String, String, Date) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
DefaultTreeDocument(Element) - Constructor for class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument: XML deserialization constructor.
delete(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence
delete(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
delete(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Returns a copy of this SequenceCharSequence where the characters at positions deletionBegin inclusive to deletionEnd exclusive have been removed.
delete(String, char) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Creates a new string identical to stringToDeleteCharacterFrom except with all instances of the given character removed.
DELETED_DOCUMENT_ORIGINAL_LOCATION_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The folder from which a deleted document originally came from
deleteDirectory(File, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Recursively deletes a directory.
deleteDocuments(List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.databaseservice.PartiallyWritableDatabaseService: Deletes documents in this database.
deleteFileOrDirectory(File, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Deletes the given file or directory.
deleteFileOrDirectory(File, FileUtilities.RetryPolicy) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Deletes the given file or directory.
deleteSelectedAnnotations() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Deletes the selected annotations if possible.
DependentComboboxSearchOption - Class in com.biomatters.geneious.publicapi.databaseservice: Allows one combo box to have a set of possible values depending on the selected value of another combo box option.
DependentComboboxSearchOption(String, String, Map<String, String[]>, Map<String, String>, String) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.DependentComboboxSearchOption: Default constructor.
dependentPreferences - Variable in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousDependentPreference: Deprecated.

The preferences which are enabled or disabled depending on the value of the GeneiousPreferences.GeneiousDependentPreference.controlPreference
DESC - Static variable in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
DESCRIPTION_CODE - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentHistoryEntryField: This code should be used in a field that provides a brief description for the entry.
DESCRIPTION_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Visible, editable field representing a document's description.
DESCRIPTION_QUALIFIER - Static variable in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: The name of a qualifier (whose value can be obtained from SequenceTrack.getQualifiers() that describes this track.
DialogButtonPanel - Class in com.biomatters.geneious.publicapi.components: A panel used to lay out buttons at the bottom of a dialog.
DialogButtonPanel(Action, Action, Action...) - Constructor for class com.biomatters.geneious.publicapi.components.DialogButtonPanel
Dialogs - Class in com.biomatters.geneious.publicapi.components: A utility class for displaying dialogs, similar to JOptionPane but with added functionality.
Dialogs.DialogAction - Class in com.biomatters.geneious.publicapi.components: Used to specify the properties of a button in a dialog.
Dialogs.DialogAction(String) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogAction
Dialogs.DialogIcon - Enum in com.biomatters.geneious.publicapi.components: Specifies the icon to display on the left hand side of a dialog.
Dialogs.DialogOptions - Class in com.biomatters.geneious.publicapi.components: A class that speicifies all the options for displaying a dialog.
Dialogs.DialogOptions(Dialogs.DialogOptions) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: contstructs a new DialogOptions based on the given source.
WARNING: this is a shallow copy, rather than a deep copy
Dialogs.DialogOptions(Dialogs.DialogOptions, Dialogs.DialogAction, Dialogs.DialogAction) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: contstructs a new DialogOptions based on the given source.
WARNING: this is a shallow copy, rather than a deep copy
Dialogs.DialogOptions(String[], String) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions
Dialogs.DialogOptions(Dialogs.DialogAction[], String) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions
Dialogs.DialogOptions(String[], String, Component) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions
Dialogs.DialogOptions(Dialogs.DialogAction[], String, Component) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions
Dialogs.DialogOptions(String[], String, Component, Dialogs.DialogIcon) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions
Dialogs.DialogOptions(Dialogs.DialogAction[], String, Component, Dialogs.DialogIcon) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions
Dialogs.Result - Class in com.biomatters.geneious.publicapi.components: The result of showing an "apply to all" dialog.
Dialogs.Result(Object, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.Result
Dialogs.SaveChanges - Enum in com.biomatters.geneious.publicapi.components: The options that the user can click on in the dialog shown by Dialogs.showSaveChangesDialog(String, java.awt.Component).
DISAGREEMENTS - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The number of alignment columns with a disagreement between two or more sequences (including internal gap vs non-gap)
All small SequenceAlignmentDocuments have this field.
discardReferences(boolean) - Method in interface com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor.DiscardReferencesCallback: indicates that values returned from a previous call to PropertyRetrieverAndEditor#getVisibleAnnotations(PropertyRetrieverAndEditor.DiscardReferencesCallback) are about to become invalidated and any references to them must be discarded.
doAlignment(List<SequenceDocument>, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Prompts the user to perform an alignment using any of the available alignment plugins.
DOCUMENT_LIST_FLAVOR - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: The DataFlavor that Geneious creates for drag-and-drop events containing Annotated Plugin Documents.
DOCUMENT_TYPE_FIELD - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: A field used for searching databases based on the document type.
DocumentAction - Class in com.biomatters.geneious.publicapi.plugin: A DocumentAction performs some operation to modify a document, without creating new documents.
DocumentAction() - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentAction
documentChanged(Element) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Replaces the contents of this document.
documentChanged(AnnotatedPluginDocument, boolean) - Method in interface com.biomatters.geneious.publicapi.documents.DocumentListener: This method is fired by a document whenever it is changed.
DocumentCollection - Class in com.biomatters.geneious.publicapi.documents: This class provides a field based document that stores a collection of other documents.
DocumentCollection() - Constructor for class com.biomatters.geneious.publicapi.documents.DocumentCollection
documentCopyAboutToBeAdded(AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceListener: Called when a document is about to be added to a WritableDatabaseService.
DocumentField - Class in com.biomatters.geneious.publicapi.documents: A Document Field describes the properties (but not value) of one data item of a plugin document or one field in a search query.
DocumentField() - Constructor for class com.biomatters.geneious.publicapi.documents.DocumentField: Empty constructor used only during XML serialisation.
DocumentField(String, String, String, Class, boolean, boolean) - Constructor for class com.biomatters.geneious.publicapi.documents.DocumentField: Constructs and initialises a DocumentField.
DocumentField.SequenceType - Enum in com.biomatters.geneious.publicapi.documents: Possible values for the DocumentField.SEQUENCE_TYPE field.
DocumentFieldAndValue - Class in com.biomatters.geneious.publicapi.documents: Wraps a DocumentField together with its value.
DocumentFieldAndValue(DocumentField, Object) - Constructor for class com.biomatters.geneious.publicapi.documents.DocumentFieldAndValue: Construct a DocumentField together with its value.
DocumentFileExporter - Class in com.biomatters.geneious.publicapi.plugin: An exporter writes Geneious documents into external files.
DocumentFileExporter() - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentFileExporter
DocumentFileExporterAndExternalViewer - Class in com.biomatters.geneious.publicapi.plugin: A file exporter with an associated external viewer.
DocumentFileExporterAndExternalViewer() - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentFileExporterAndExternalViewer
DocumentFileImporter - Class in com.biomatters.geneious.publicapi.plugin: An importer reads external files and converts the contents to Geneious documents.
DocumentFileImporter() - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter
DocumentFileImporter.AutoDetectStatus - Enum in com.biomatters.geneious.publicapi.plugin: Possible results of file type auto detection.
DocumentFileImporter.ImportCallback - Class in com.biomatters.geneious.publicapi.plugin
DocumentFileImporter.ImportCallback() - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.ImportCallback
DocumentHistory - Class in com.biomatters.geneious.publicapi.documents: The document history for an AnnotatedPluginDocument is made up of a list of entries.
DocumentHistoryEntry - Class in com.biomatters.geneious.publicapi.documents: Represents a single 'edit' of a document in the document history.
DocumentHistoryEntryField - Class in com.biomatters.geneious.publicapi.documents: A document history field is basically a name-value pair that describes one aspect of a DocumentHistoryEntry.
documentIcon - Variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: An icon associated with documents of that type.
DocumentImportException - Exception in com.biomatters.geneious.publicapi.plugin: An exception thrown when import of document fails due to improper format or unexpected data in file.
DocumentImportException(String) - Constructor for exception com.biomatters.geneious.publicapi.plugin.DocumentImportException: constructor.
DocumentImportException(String, Throwable) - Constructor for exception com.biomatters.geneious.publicapi.plugin.DocumentImportException: Constructs a new documentImportException with the specified detail message and cause.
DocumentImportException.Canceled - Exception in com.biomatters.geneious.publicapi.plugin: Represents a DocumentFileImporter that has failed because it has been canceled.
DocumentImportException.Canceled() - Constructor for exception com.biomatters.geneious.publicapi.plugin.DocumentImportException.Canceled
DocumentListener - Interface in com.biomatters.geneious.publicapi.documents: Used for notifying when an AnnotatedPluginDocument has changed.
documentMoved(AnnotatedPluginDocument, DatabaseService) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceListener: Called when a document is moved using WritableDatabaseService.moveDocument(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, jebl.util.ProgressListener).
DocumentNote - Interface in com.biomatters.geneious.publicapi.documents: Represents an instance of a DocumentNoteType that exists on a document.
DocumentNoteField - Class in com.biomatters.geneious.publicapi.documents: Describes the properties of a single value in a note.
DocumentNoteField.Types - Enum in com.biomatters.geneious.publicapi.documents: All of the available note field types.
DocumentNoteType - Interface in com.biomatters.geneious.publicapi.documents: This represents a "Note Type" in the program.
DocumentNoteUtilities - Class in com.biomatters.geneious.publicapi.documents: This gives access to the NoteTypes defined in the program.
DocumentOperation - Class in com.biomatters.geneious.publicapi.plugin: A DocumentOperation creates a new document from a set of existing documents (or from no documents).
The DocumentOperation displays an optional OptionsPanel (a JPanel), and then performs an operation on the set of documents that the user has selected.
DocumentOperation() - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentOperation
DocumentOperation.OperationCallback - Class in com.biomatters.geneious.publicapi.plugin: Provides a callback facility to DocumentOperations.
DocumentOperation.OperationCallback() - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback
DocumentOperation.OperationCallback.Wrapper - Class in com.biomatters.geneious.publicapi.plugin: Creates a wrapper OperationCallback that delegates all methods to another OperationCallback
DocumentOperation.OperationCallback.Wrapper(DocumentOperation.OperationCallback) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback.Wrapper
DocumentOperation.Wrapper - Class in com.biomatters.geneious.publicapi.plugin: Provides a wrapper DocumentOperation that delegates all methods (except DocumentOperation.getUniqueId()) to the wrapped operation.
DocumentOperation.Wrapper(DocumentOperation) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper: Constructs a new wrapper operation
DocumentOperationException - Exception in com.biomatters.geneious.publicapi.plugin: This Exception class is used for 2 distinct but related situations A DocumentOperationException is thrown when a document operation encounters unexpected problems.
DocumentOperationException(String) - Constructor for exception com.biomatters.geneious.publicapi.plugin.DocumentOperationException: See Exception.Exception()
DocumentOperationException(String, Throwable) - Constructor for exception com.biomatters.geneious.publicapi.plugin.DocumentOperationException: See Exception.Exception(String, Throwable)
DocumentOperationException(Throwable) - Constructor for exception com.biomatters.geneious.publicapi.plugin.DocumentOperationException: See Exception.Exception(Throwable)
DocumentOperationException.Canceled - Exception in com.biomatters.geneious.publicapi.plugin: Represents a DocumentOperation or SequenceAnnotationGenerator that has failed because it has been canceled.
DocumentOperationException.Canceled() - Constructor for exception com.biomatters.geneious.publicapi.plugin.DocumentOperationException.Canceled: See DocumentOperationException.Canceled
DocumentOperationInput - Class in com.biomatters.geneious.publicapi.plugin: Represents input to a DocumentOperation.
DocumentOperationInput(List<AnnotatedPluginDocument>) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentOperationInput: Constructs new DocumentOperationInput.
DocumentOperationInput(AnnotatedPluginDocument...) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentOperationInput: Constructs new DocumentOperationInput.
DocumentSearchCache<T extends PluginDocument> - Class in com.biomatters.geneious.publicapi.documents: Class which caches the results of a search for a particular type of document and automatically updates to include newly added documents of the particular type when they are added to the user's database.
DocumentSelectionOption - Class in com.biomatters.geneious.publicapi.plugin: An option to allow the user to select a number of documents of a particular type from their local database.
DocumentSelectionOption.FolderOrDocuments - Class in com.biomatters.geneious.publicapi.plugin: The value type for DocumentSelectionOption which represents either a list of selected documents or a single selected folder which contains some documents of the correct type.
DocumentSelectionOption.FolderOrDocuments(WritableDatabaseService) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.FolderOrDocuments: Create a FolderOrDocuments for a folder selection
DocumentSelectionOption.FolderOrDocuments(List<AnnotatedPluginDocument>) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.FolderOrDocuments: Create a FolderOrDocuments for a selection of documents
DocumentSelectionOption.FolderOrDocuments(AnnotatedPluginDocument) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.FolderOrDocuments: Create a FolderOrDocuments for a selection of one document
DocumentSelectionSignature - Class in com.biomatters.geneious.publicapi.plugin: Several plugin components (Viewers, Exporters, Operations, Actions) operate on one (or a set of) Geneious documents.
DocumentSelectionSignature(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: XML deserialization constructor
DocumentSelectionSignature(DocumentSelectionSignature.DocumentSelectionSignatureAtom[]) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: construct signature from given atoms.
DocumentSelectionSignature(DocumentSelectionSignature.DocumentSelectionSignatureAtom) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: convenience constructor.
DocumentSelectionSignature(Class, int, int) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: convenience constructor for accepting a single class repeated a certain number of times.
DocumentSelectionSignature.DocumentSelectionSignatureAtom - Class in com.biomatters.geneious.publicapi.plugin: A signature is a set of Atoms.
DocumentSelectionSignature.DocumentSelectionSignatureAtom(Class, int, int) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature.DocumentSelectionSignatureAtom: constructor.
DocumentType<T> - Class in com.biomatters.geneious.publicapi.plugin: Declares one Geneious plugin document type used for associating icons and human readable names with PluginDocument classes.
DocumentType(String, Class<T>, Icons) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentType: constructor.
DocumentType(String, Class<T>, Class, Icons) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentType
DocumentUtilities - Class in com.biomatters.geneious.publicapi.documents: Some core functionality provided by Geneious for adding and managing documents.
DocumentViewer - Class in com.biomatters.geneious.publicapi.plugin: A viewer displays one (or more) Geneious documents to the user.
DocumentViewer() - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentViewer
DocumentViewer.ViewerLocation - Class in com.biomatters.geneious.publicapi.plugin: Information about the location of a viewer eg.
DocumentViewer.ViewerLocation(boolean, boolean, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentViewer.ViewerLocation
DocumentViewerFactory - Class in com.biomatters.geneious.publicapi.plugin: A DocumentViewerFactory creates a DocumentViewer which displays one or more Geneious documents to the user.
DocumentViewerFactory() - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory
DocumentViewerFactory.ViewPrecedence - Enum in com.biomatters.geneious.publicapi.plugin: Viewer precedence level.
DocumentViewerMessageHandler - Class in com.biomatters.geneious.publicapi.plugin: DocumentViewers occasionally wish to interact with each other.
DocumentViewerMessageHandler() - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentViewerMessageHandler
DONT_INITIALLY_FOCUS_KEY - Static variable in class com.biomatters.geneious.publicapi.components.Dialogs: By calling putClientProperty() on a JTextField with this as the key and Boolean.TRUE as the value, calling code may ensure that this text field never gets initially focussed (showOptionsDialog() and showTextFieldDialog() automatically focus the topmost, non-flagged textfield in the dialog).
doubleValue() - Method in class com.biomatters.geneious.publicapi.implementations.EValue
doubleValue() - Method in class com.biomatters.geneious.publicapi.implementations.Percentage
draw(GeneiousGraphics2D, int, int, int, int, int, int, double, int, int, int, int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Draws a section of this graph.
drawBorderForTopComponent(Component, Component, Graphics) - Static method in class com.biomatters.geneious.publicapi.components.OptionsPanel.RoundedLineBorder: For a headless line border, draws the border for the top component (placed directly above the component with the line border, e.g.
drawLine(int, int, int, int) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics.drawLine(int, int, int, int)
drawOval(int, int, int, int) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics.drawOval(int, int, int, int)
drawPolygon(Polygon) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics.drawPolygon(java.awt.Polygon).
drawPolyLine(int[], int[], int) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics.drawPolyline(int[], int[], int)
drawRect(int, int, int, int) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics.drawRect(int, int, int, int)
drawRoundRect(int, int, int, int, int, int) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics.drawRoundRect(int, int, int, int, int, int)
drawScaleBar(GeneiousGraphics2D, int, int, int, int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Optionally draw a scale bar next to the name of the graph.
drawString(String, int, int) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics2D.drawString(String, int, int).
drawStringCentred(String, int, int) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: Just like Graphics2D.drawString(String,int,int) except that the text is centred at centreX , centreY
drawStringWithinBounds(String, int, int, int, int, boolean) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: draws the given text squashed or stretched into the given dimensions at the given location
duplicateDocument(AnnotatedPluginDocument, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Create a duplicate of document.
duplicateDocumentAndDealWithReferencedDocuments(AnnotatedPluginDocument, ElementProvider, AtomicReference<Element>) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Deprecated.
use #duplicateDocumentAndDealWithReferencedDocuments
duplicateDocumentAndDealWithReferencedDocuments(AnnotatedPluginDocument, ElementProvider, AtomicReference<Element>, URN) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: This as a helper method to facilitate implementing WritableDatabaseService._addDocumentCopy(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument,jebl.util.ProgressListener).
duplicateDocumentThrowingDocumentOperationExceptionOnFailure(AnnotatedPluginDocument, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Create a duplicate of document.

E

EditableNucleotideGraphSequenceDocument - Interface in com.biomatters.geneious.publicapi.documents.sequence: A mutable nucleotide sequence with residue graph.
EditableSameTaxaTreesDocument - Interface in com.biomatters.geneious.publicapi.documents.types: A mutable tree set.
EditableSequenceDocument - Interface in com.biomatters.geneious.publicapi.documents.sequence: An extensions of a SequenceDocument that can be edited.
EditableSequenceListDocument - Interface in com.biomatters.geneious.publicapi.documents.sequence: A SequenceListDocument that can have its internal lists of nucleotide and amino acid sequences reordered, added to, or removed from.
editDocumentField(AnnotatedPluginDocument, DocumentFieldAndValue) - Method in class com.biomatters.geneious.publicapi.databaseservice.PartiallyWritableDatabaseService: Edits a field value on a document.
EDITING_HISTORY - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup: A group of annotations created when a sequence is manually editing, including SequenceAnnotation.TYPE_EDITING_HISTORY_REPLACEMENT, SequenceAnnotation.TYPE_EDITING_HISTORY_INSERTION, SequenceAnnotation.TYPE_EDITING_HISTORY_DELETION.
EDITING_HISTORY_ORIGINAL_BASES - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Record the bases that were originally in the location covered by an annotation of type SequenceAnnotation.TYPE_EDITING_HISTORY_DELETION, SequenceAnnotation.TYPE_EDITING_HISTORY_INSERTION or SequenceAnnotation.TYPE_EDITING_HISTORY_REPLACEMENT.
editSelectedAnnotations() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Opens the annotation editing dialog for the currently selected annotations.
element - Variable in class com.biomatters.geneious.publicapi.documents.URN: The specified media element.
ElementProvider - Interface in com.biomatters.geneious.publicapi.documents: Provides a method to load an XML element with progress information and the ability to cancel it.
EMPTY - Static variable in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback
EMPTY - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: An empty (0 length) immutable SequenceCharSequence
EMPTY - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.FolderOrDocuments: Represents an empty selection
EMPTY - Static variable in class com.biomatters.geneious.publicapi.utilities.Execution.OutputListener: An OutputListener which ignores all output.
enableValues - Variable in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousDependentPreference: Deprecated.

The set of values for which the GeneiousPreferences.GeneiousDependentPreference.controlPreference must be in one of for the GeneiousPreferences.GeneiousDependentPreference.dependentPreferences to be enabled.
encode(byte[]) - Static method in class com.biomatters.geneious.publicapi.utilities.Base64Coder: Encodes a byte array into Base64 format.
endAlignHorizontally() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Finishes a previously started row of horizontally aligned options (see Options.beginAlignHorizontally(String, boolean).
endBorderedGroup() - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: If we are adding components to a sub panel (see OptionsPanel.beginBorderedGroup(String, boolean)), then close off the current sub panel.
endElement(String, String, String) - Method in class com.biomatters.geneious.publicapi.utilities.xml.FilteredSaxHandler
EndGapsHelper - Class in com.biomatters.geneious.publicapi.implementations: Calculates, and provides a method to determine whether residues in a set of sequences are end gaps.
EndGapsHelper(CharSequence[], boolean) - Constructor for class com.biomatters.geneious.publicapi.implementations.EndGapsHelper: Construct some new end gaps.
EndGapsManager - Class in com.biomatters.geneious.publicapi.implementations: Given a set of aligned sequences, provides methods for quickly finding all sequences that intersect a given base number, ignoring those sequences in end gap regions.
EndGapsManager(EndGapsManager, SequenceCharSequence) - Constructor for class com.biomatters.geneious.publicapi.implementations.EndGapsManager: Creates a new EndGapsManager identical to the provided one except for the addition of a reference sequence at index 0.
EndGapsManager(Element, SequenceListOnDisk<SequenceDocument>) - Constructor for class com.biomatters.geneious.publicapi.implementations.EndGapsManager: Recreates an EndGapsManager from XML.
EndGapsManager(SequenceCharSequence[], int) - Constructor for class com.biomatters.geneious.publicapi.implementations.EndGapsManager
EndGapsManager(SequenceCharSequence[], int, int) - Constructor for class com.biomatters.geneious.publicapi.implementations.EndGapsManager
EndGapsManager(List<SequenceCharSequence>, int, int) - Constructor for class com.biomatters.geneious.publicapi.implementations.EndGapsManager
EndGapsManager(SequenceAlignmentDocument, int) - Constructor for class com.biomatters.geneious.publicapi.implementations.EndGapsManager: Creates an EndGapsManager for the sequences in the given alignment.
EndGapsManager.Builder - Class in com.biomatters.geneious.publicapi.implementations: Used for building an EndGapsManager which is too large to fit in memory
EndGapsManager.Builder() - Constructor for class com.biomatters.geneious.publicapi.implementations.EndGapsManager.Builder: Construct a new Builder.
ensureMemoryAvailable(long) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Ensures that at least this much memory is available plus a little extra (10 MB in the current implementation) to be safe, and if not throws an XMLSerializationException
ensureRectangleIsWithinBounds(Rectangle, Rectangle) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: If the given rectangle is not completely contained within maximumBounds then move it the smallest possible distance so that it is.
ensureWindowIsOnScreen(Window) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: If the given window is not completely contained within a single screen then move it the smallest possible distance so that it is.
ENTER_KEY_STRING - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: System-dependent string used to represent the ENTER/RETURN key
equals(Object) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogAction
equals(Object) - Method in class com.biomatters.geneious.publicapi.databaseservice.QueryField
equals(Object) - Method in class com.biomatters.geneious.publicapi.documents.DocumentField
equals(Object) - Method in class com.biomatters.geneious.publicapi.documents.DocumentFieldAndValue
equals(Object) - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField
equals(Object) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument.ReferencedSequence
equals(Object) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
equals(Object) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup
equals(Object) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval
equals(Object) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
equals(Object) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Checks whether obj is a SequenceCharSequence representing the same sequence of characters as this one.
equals(Object) - Method in class com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument.Taxon
equals(Object) - Method in class com.biomatters.geneious.publicapi.documents.URN: Returns true if this URN and the object argument represent the same URN.
equals(Object) - Method in class com.biomatters.geneious.publicapi.implementations.Percentage
equals(Object) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.FolderOrDocuments
equals(Object) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature.DocumentSelectionSignatureAtom: compare two atoms.
equals(Object) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentType
equals(Object) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
equals(Object) - Method in class com.biomatters.geneious.publicapi.plugin.License.PluginLicense
equals(Object) - Method in class com.biomatters.geneious.publicapi.plugin.Options.OptionValue: Two OptionValue's are considered equal with if only if their names are equal
equals(Object) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection
equals(Object) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
equals(Object) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex
equals(CharSequence, CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities: Checks whether two CharSequences contain the same sequence of characters.
equals(Object) - Method in class com.biomatters.geneious.publicapi.utilities.Interval
equalsIgnoreCase(SequenceCharSequence) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Checks whether this SequenceCharSequence contains the same sequence of characters as the specified SequenceCharSequence, ignoring case.
equalsIgnoreCase(CharSequence, CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities: Checks whether two CharSequences contain the same sequence of characters, ignoring case.
EValue - Class in com.biomatters.geneious.publicapi.implementations: Just like a double, but the toString() method displays it as a nicely formatted e value
EValue(double, int) - Constructor for class com.biomatters.geneious.publicapi.implementations.EValue
EValue() - Constructor for class com.biomatters.geneious.publicapi.implementations.EValue: this constructor is only here to be used immediately prior to fromXML.
EValue(double) - Constructor for class com.biomatters.geneious.publicapi.implementations.EValue
exclude(Element) - Method in interface com.biomatters.geneious.publicapi.documents.AdditionalSearchContent.Utilities.FilterElement
execute() - Method in class com.biomatters.geneious.publicapi.utilities.Execution: Starts execution of the external program represented by this object.
execute(Map<String, String>) - Method in class com.biomatters.geneious.publicapi.utilities.Execution: Starts execution of the external program represented by this object.
Execution - Class in com.biomatters.geneious.publicapi.utilities: Executes an external program.
Execution(String[], Cancelable, Execution.OutputListener, String, boolean) - Constructor for class com.biomatters.geneious.publicapi.utilities.Execution: Constructs an Execution object that represents an execution of an external program.
Execution(String[], Cancelable, Execution.OutputListener, InputStream, boolean) - Constructor for class com.biomatters.geneious.publicapi.utilities.Execution: Constructs an Execution object that represents an execution of an external program.
Execution.OutputListener - Class in com.biomatters.geneious.publicapi.utilities: Reports output received from an external process.
Execution.OutputListener() - Constructor for class com.biomatters.geneious.publicapi.utilities.Execution.OutputListener
export(ExportableDocument.Format, OutputStream) - Method in interface com.biomatters.geneious.publicapi.documents.ExportableDocument: Export a document.
export(ExportableDocument.Format, OutputStream) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
export(ExportableDocument.Format, OutputStream) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
export(ExportableDocument.Format, OutputStream) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
export(File, PluginDocument[], ProgressListener, Options) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileExporter: Do the actual exporting from PluginDocuments.
export(File, AnnotatedPluginDocument[], ProgressListener, Options) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileExporter: Do the actual exporting.
ExportableDocument - Interface in com.biomatters.geneious.publicapi.documents: Interface implemented by plugin documents that wish to implemenet a specialized export.
ExportableDocument.Format - Enum in com.biomatters.geneious.publicapi.documents: Current exportable formats.
exportDocuments(File, AnnotatedPluginDocument...) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Exports these documents to this file in a format suitable for the given file's extension.
exportDocumentsInGeneiousFormat(File, boolean, AnnotatedPluginDocument...) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Exports the given documents in Geneious format (zip compressed), to the given file.
exportDocumentsInGeneiousFormat(File, ProgressListener, AnnotatedPluginDocument...) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Exports the given documents in Geneious format (zip compressed), to the given file.
exportDocumentsInGeneiousFormat(OutputStream, ProgressListener, AnnotatedPluginDocument...) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Exports the given documents in Geneious format (zip compressed), to the given output stream.
ExtendedEditableSequenceListDocument - Interface in com.biomatters.geneious.publicapi.documents.sequence: Similar to an EditableSequenceListDocument but also allows replacing sequences with new sequences or modifying the contents of individual sequences
ExtendedNucleotideGraph - Interface in com.biomatters.geneious.publicapi.documents.sequence: Provides an extended interface to a NucleotideGraph.
ExtendedPrintable - Class in com.biomatters.geneious.publicapi.plugin: An alternative to Printable which provides additional information and options which also provides useful information when saving to an image.
ExtendedPrintable() - Constructor for class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable
ExtendedPrintable.Factory - Class in com.biomatters.geneious.publicapi.plugin: Provides factory methods for creating ExtendedPrintables
ExtendedPrintable.Wrapper - Class in com.biomatters.geneious.publicapi.plugin: Wrapper that delegates all methods to the source ExtendedPrintable.
ExtendedPrintable.Wrapper(ExtendedPrintable) - Constructor for class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Wrapper
ExtendedSearchOption - Class in com.biomatters.geneious.publicapi.databaseservice: Base interface for extended search options.
ExtendedSearchOption(String, String) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.ExtendedSearchOption
extendedSearchOptionsChanged() - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceListener: Notify the code using this database that this database's extended options have changed.
EXTENSION_QUALIFIER_NAME - Static variable in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Name to use for SequenceAnnotationQualifiers that specify any primer extension sequence in addition to the primer binding region.
ExternalSort<T> - Class in com.biomatters.geneious.publicapi.documents.sequence: Sorts some objects, using temporary files on disk if necessary because the objects can't all fit in memory (e.g.
ExternalSort(ExternalSort.Serializer<T>, Comparator<T>, ProgressListener, int) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.ExternalSort
ExternalSort.Serializer<T> - Interface in com.biomatters.geneious.publicapi.documents.sequence: Specifies how to serialize the elements to disk and read them back in again.
extract(SequenceDocument, SequenceExtractionUtilities.ExtractionOptions) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Extracts one or more intervals from a sequence as a new sequence document.
extract(StringBuilder) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Extracts the result of a StringBuilder using less memory than StringBuilder.toString().
EXTRACTED_REGION_INTERVALS_NAME - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Name to use for a SequenceAnnotationQualifier to specify that the SequenceAnnotation represents an extraction (annotations of type SequenceAnnotation.TYPE_EXTRACTED_REGION The value of the qualifier is parsable using SequenceAnnotationInterval.SequenceAnnotationInterval(String).
EXTRACTED_REGION_ORIGINAL_CIRCULAR_SEQUENCE_LENGTH - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Name to use for a SequenceAnnotationQualifier to specify that the SequenceAnnotation represents an extraction (annotations of type SequenceAnnotation.TYPE_EXTRACTED_REGION from a circular sequence, in which case, this qualifier contains the length of the original circular sequence.
extractIntervals(SequenceDocument, SequenceAnnotationInterval...) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: A convenience method for extracting intervals from a sequence.
extractIntervals(SequenceDocument, Interval...) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: A convenience method for extracting intervals from a sequence.
extractIntervals(SequenceDocument, String, GeneticCode, int, boolean, List<SequenceAnnotationInterval>, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Deprecated.
use SequenceExtractionUtilities.extractIntervals(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions) instead.
extractIntervals(SequenceDocument, SequenceExtractionUtilities.ExtractionOptions) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Extracts one or more intervals from a sequence as a new sequence document.
extractIntervals() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection: Deprecated.
extractIntervalsOrThrow(SequenceDocument, SequenceExtractionUtilities.ExtractionOptions) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Extracts one or more intervals from a sequence as a new sequence document.
extractOrThrow(SequenceDocument, SequenceExtractionUtilities.ExtractionOptions) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Extracts one or more intervals from a sequence as a new sequence document.

F

FastSaxBuilder - Class in com.biomatters.geneious.publicapi.utilities.xml: A Sax Builder that is faster and uses less memory than the standard sax builder it extends (SAXBuilder).
FastSaxBuilder() - Constructor for class com.biomatters.geneious.publicapi.utilities.xml.FastSaxBuilder
field - Variable in class com.biomatters.geneious.publicapi.databaseservice.QueryField: Field to search on.
fieldsChanged() - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceListener: Notify using code about a change in search fields.
fieldsFromElement(Element, Map<String, Object>) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Restore values stored in element by XMLSerializer.fieldValuesToElement(java.lang.String, java.util.Map<java.lang.String, java.lang.Object>).
fieldValuesToElement(String, Map<String, Object>) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Create one jdom element containing several fields.
fieldValuesToElement(Geneious.MajorVersion, String, Map<String, Object>, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Create one jdom element containing several fields.
fieldValueToElement(String, Object) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Create one jdom element containing one field value.
fieldValueToElement(Geneious.MajorVersion, String, Object) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Create one jdom element containing one field value.
FILE_DATA_ATTRIBUTE_NAME - Static variable in interface com.biomatters.geneious.publicapi.documents.PluginDocument: A PluginDocument may choose to serialize some or all of its data to a file instead of to in memory XML.
FileUtilities - Class in com.biomatters.geneious.publicapi.utilities: Provides utility methods for dealing with files.
FileUtilities.RetryPolicy - Enum in com.biomatters.geneious.publicapi.utilities: Specifies a policy about what to do if a file action (e.g.
FileUtilities.TargetExistsAction - Enum in com.biomatters.geneious.publicapi.utilities: The action to take when moving/copying files and the target already exists
fillOval(int, int, int, int) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics.fillOval(int, int, int, int)
fillPolygon(Polygon) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics.fillPolygon(java.awt.Polygon)
fillRect(int, int, int, int) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics.fillRect(int, int, int, int)
fillRoundRect(int, int, int, int, int, int) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics.fillRoundRect(int, int, int, int, int, int)
FilteredSaxHandler - Class in com.biomatters.geneious.publicapi.utilities.xml: A Sax Handler that provides full jdom Elements for specified element names.
FilteredSaxHandler(List<String>, FilteredSaxHandler.ElementHandler, long) - Constructor for class com.biomatters.geneious.publicapi.utilities.xml.FilteredSaxHandler: Creates a sax handler that provides elements matching a given name pattern to a callback.
FilteredSaxHandler.ElementHandler - Interface in com.biomatters.geneious.publicapi.utilities.xml
finalize() - Method in class com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout
finalize() - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager
find(Findable.FindOptions) - Method in class com.biomatters.geneious.publicapi.plugin.Findable: Performs a find using the given options.
find(Findable.FindOptions, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.Findable: A Findable implementation may optionally implement this variation of Findable.find(com.biomatters.geneious.publicapi.plugin.Findable.FindOptions) if it may take a noticable amount of time to perform the search.
Findable - Class in com.biomatters.geneious.publicapi.plugin: May be supplied by a document viewer (via getFindable()) to support textual searching inside the viewer.
Findable() - Constructor for class com.biomatters.geneious.publicapi.plugin.Findable
Findable.FindOptions - Class in com.biomatters.geneious.publicapi.plugin: User options for a search.
Findable.FindOptions(String, boolean, boolean, boolean, Options) - Constructor for class com.biomatters.geneious.publicapi.plugin.Findable.FindOptions: This constructor must only be called by Geneious; do not call it from a plugin!
finishedAddingSequences(ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Indicates that SequenceListSummary.addSequence(SequenceDocument) will no longer be called, and builds and sorts the summary data.
finishedAddingValues(ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution: Called to finalize and sort the data.
finishedProcessing(T) - Method in class com.biomatters.geneious.publicapi.utilities.MultiThreadedProcessingSystem: An implementation may optionally override this to perform any additional cleanup.
fire() - Method in class com.biomatters.geneious.publicapi.utilities.WeakSimpleListenerManager
fireActionListeners() - Method in class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption: calls the ActionListener.actionPerformed(java.awt.event.ActionEvent) methods of all ActionListener objects added to this option by calling Options.ButtonOption.addActionListener(java.awt.event.ActionListener).
firePluginChangedListeners() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: Sub-classes should use this method to notify all listeners added using GeneiousPlugin.addPluginChangedListener(org.virion.jam.util.SimpleListener) that they have change their provided operations, services etc.
fireSelectedAnnotationsChangedListeners() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Fires all listeners added using SequenceViewerExtension.PropertyRetrieverAndEditor.addSelectedAnnotationsChangedListener(org.virion.jam.util.SimpleListener)
fireSelectionChanged(TreeSelectionChangeEvent) - Method in class com.biomatters.geneious.publicapi.plugin.TreeViewerExtension: A TreeViewerExtension should called this method to notify the tree viewer plug-in that it wants to modify the set of selected nodes in the current tree.
fireTreeChanged(TreeChangeEvent) - Method in class com.biomatters.geneious.publicapi.plugin.TreeViewerExtension: A TreeViewerExtension should called this method to notify the tree viewer plug-in that it wants to modify the tree being viewed.
fireVisibleAnnotationsChangedListeners() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Fires all listeners added using SequenceViewerExtension.PropertyRetrieverAndEditor.addVisibleAnnotationsChangedListener(org.virion.jam.util.SimpleListener)
FIRST_SEQUENCE_RESIDUES - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The first few residues or bases in a sequence.
fitToScreen() - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: A convenience method for setZoomLevel(zoomPanel.getFitToScreenZoomLevel())
floatValue() - Method in class com.biomatters.geneious.publicapi.implementations.EValue
floatValue() - Method in class com.biomatters.geneious.publicapi.implementations.Percentage
flush() - Method in class com.biomatters.geneious.publicapi.utilities.OutputStreamThatCountsBytesWritten
FolderView - Class in com.biomatters.geneious.publicapi.databaseservice: Stores information about documents in a folder.
FolderView(List<DocumentField>, DocumentField) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.FolderView: Constuct a new FolderView
FolderView(Element) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.FolderView: XML deserialization constructor.
FolderViewDocument - Interface in com.biomatters.geneious.publicapi.databaseservice: A PluginDocument may implement this interface to indicate that it provides information about the results of a search.
forAlignment(SequenceAlignmentDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever: Creates a SequencePropertyRetriever for this alignment.
forAlignment(SequenceAlignmentDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Creates a SequencePropertyRetriever for an alignment.
forAminoAcidSequences(List<AminoAcidSequenceDocument>) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: Construct a new DefaultSequenceListDocument.
forBothSequenceTypes(List<NucleotideSequenceDocument>, List<AminoAcidSequenceDocument>) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: Construct a new DefaultSequenceListDocument.
forBothSequenceTypes(List<NucleotideSequenceDocument>, List<AminoAcidSequenceDocument>, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: Construct a new DefaultSequenceListDocument.
forBothSequenceTypes(List<? extends SequenceDocument>, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: Construct a new DefaultSequenceListDocument.
forInclusiveRange(int, int) - Static method in class com.biomatters.geneious.publicapi.utilities.Interval: Constructs an interval where the 2nd value is inclusive rather than exclusive.
formatDateNicely(Date, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Nicely formats a Date in the Geneious style.
formatElement(Element) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Prints an Element in pretty format (Format.getPrettyFormat()) to a String and returns that String.
formatElementPreserveText(Element) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Prints an Element in pretty format similar to (Format.getPrettyFormat()) and returns that String.
formatElementRaw(Element) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Prints an Element in raw format (Format.getRawFormat()) to a String and returns that String.
formatStackTrace(Throwable) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Prints the stacktrace associated with a Throwable to a String and returns the String.
forName(String) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Deprecated.
use PluginUtilities.getClass(String) instead.
forNucleotideAlignment(int, int) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: Creates a selection signature that matches a single alignment that contains a specified range of nucleotide sequences.
forNucleotideAlignments(int, int) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: Creates a selection signature that matches a number of nucleotide SequenceAlignmentDocuments within the given range.
forNucleotideAndProteinSequences(int, int, int, int, boolean) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: Creates a selection signature that matches any combination of SequenceListDocument, SequenceAlignmentDocument (if allowSequencesInAlignments is true), NucleotideSequenceDocument and AminoAcidSequenceDocument such that the total number of nucleotide sequences they contain is within the given range and the total number of protein sequences is also within the range.
forNucleotideSequences(List<NucleotideSequenceDocument>) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: Construct a new DefaultSequenceListDocument.
forNucleotideSequences(int, int) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: Creates a selection signature that matches any combination of SequenceListDocument and NucleotideSequenceDocument such that the total number of nucleotide sequences they contain is within the given range.
forNucleotideSequences(int, int, boolean) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: Creates a selection signature that matches any combination of SequenceListDocument, SequenceAlignmentDocument (if allowSequencesInAlignments is true) and NucleotideSequenceDocument such that the total number of nucleotide sequences they contain is within the given range, and there are no protein sequences.
forNucleotideSequencesAndAlignments(int, int, int, int) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: Creates a selection signature that matches any combination of SequenceListDocument, and NucleotideSequenceDocument such that the total number of nucleotide sequences they contain is within the given range, and there are no protein sequences.
forProteinAlignment(int, int) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: Creates a selection signature that matches a single alignment that contains a specified range of protein sequences.
forProteinAlignments(int, int) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: Creates a selection signature that matches a number of protein SequenceAlignmentDocuments within the given range
forProteinSequences(int, int, boolean) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: Creates a selection signature that matches any combination of SequenceListDocument, SequenceAlignmentDocument (if allowSequencesInAlignments is true) and AminoAcidSequenceDocument such that the total number of protein sequences they contain is within the given range, and there are no nucleotide sequences.
forProteinSequences(int, int) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: Creates a selection signature that matches any combination of SequenceListDocument and AminoAcidSequenceDocument such that the total number of protein sequences they contain is within the given range.
forProteinSequencesAndAlignments(int, int, int, int) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: Creates a selection signature that matches any combination of SequenceListDocument, and AminoAcidSequenceDocument such that the total number of protein sequences they contain is within the given range, and there are no nucleotide sequences, plus a number of protein SequenceAlignmentDocuments within the given range
forSequenceDocument(SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Get SequenceGapInformation for the given sequence.
forSequenceDocuments(AnnotatedPluginDocument...) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument.ReferencedSequence: Creates a list of ReferencedSequence, with 1 entry in the list for each given document (each of which must be a SequenceDocument) or null.
forSequences(SequenceDocument...) - Static method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Creates a SequencePropertyRetriever for a list of sequences.
forValues(int...) - Static method in class com.biomatters.geneious.publicapi.utilities.IntList: Creates a new IntList containing these values.
forValues(int[], int, int) - Static method in class com.biomatters.geneious.publicapi.utilities.IntList: Creates a new IntList containing a subset of the values in an array.
forVersion(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.Geneious.MajorVersion: Gets the MajorVersion from a full Geneious version (e.g.
freeVersionName() - Static method in class com.biomatters.geneious.publicapi.plugin.License: Deprecated.
the "free" version of Geneious no longer has a name, features are simply restricted when no license is active. Deprecated in API 4.600 (Geneious 6.0.0)
freeVersionSuffix() - Static method in class com.biomatters.geneious.publicapi.plugin.License: Deprecated.
the "free" version of Geneious no longer has a name, features are simply restricted when no license is active. Deprecated in API 4.600 (Geneious 6.0.0)
from - Variable in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature.DocumentSelectionSignatureAtom: Repeated N (from <= N < to) times.
fromJeblAlignment(Alignment) - Static method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Converts the given JEBL alignment into a DefaultAlignmentDocument.
fromName(String) - Static method in enum com.biomatters.geneious.publicapi.documents.Condition: Get the condition back from name.
fromString(String) - Static method in enum com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument.OligoType
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.databaseservice.FolderView
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.databaseservice.QueryField
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.documents.Author
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.documents.DocumentCollection
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.documents.DocumentField
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
fromXML(Element, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: Deserializes this document from XML
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
fromXml(Element) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Constructs a SequenceCharSequence from the specified element to which it was serialized via SequenceCharSequence.toXML().
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Unsupported operation.
fromXml(Element) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk: Recreates a SequenceListOnDisk from XML returned from SequenceListOnDisk.toXML(String)
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution
fromXML(Element) - Static method in class com.biomatters.geneious.publicapi.documents.URN: Convert back to URN from element generated by URN.toXML(String).
fromXML(Element) - Method in interface com.biomatters.geneious.publicapi.documents.XMLSerializable: Restore the object from the JDOM Element returned by XMLSerializable.toXML().
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.implementations.EValue
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.implementations.Percentage
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument
fromXML(Element, NucleotideGraph) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: Deprecated.
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.plugin.Options
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: See XMLSerializable.fromXML(org.jdom.Element).
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.plugin.Options.OptionValue
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.ExtractionStrategy
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.utilities.Interval
fromXml(Element, PluginDocumentXmlCollection.ElementHandler, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.xml.PluginDocumentXmlCollection: deserializes some XML elements, calling handleElement(org.jdom.Element) for each child element.

G

GarbageCollectionNotifier - Class in com.biomatters.geneious.publicapi.utilities: Provides a system for notifying when an object has been garbage collected.
GButton - Class in com.biomatters.geneious.publicapi.components: Same as JButton except not opaque on Mac OS by default.
GButton() - Constructor for class com.biomatters.geneious.publicapi.components.GButton
GButton(Icon) - Constructor for class com.biomatters.geneious.publicapi.components.GButton
GButton(String, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.GButton
GButton(String) - Constructor for class com.biomatters.geneious.publicapi.components.GButton
GButton(Action) - Constructor for class com.biomatters.geneious.publicapi.components.GButton
GButton(String, Icon) - Constructor for class com.biomatters.geneious.publicapi.components.GButton
GComboBox - Class in com.biomatters.geneious.publicapi.components: A JComboBox that provides edit menu support ( copy, paste, undo etc).
GComboBox(ComboBoxModel) - Constructor for class com.biomatters.geneious.publicapi.components.GComboBox
GComboBox(Object[]) - Constructor for class com.biomatters.geneious.publicapi.components.GComboBox
GComboBox(Vector<?>) - Constructor for class com.biomatters.geneious.publicapi.components.GComboBox
GComboBox() - Constructor for class com.biomatters.geneious.publicapi.components.GComboBox
GComboBox(boolean) - Constructor for class com.biomatters.geneious.publicapi.components.GComboBox: Construct a new GComboBox
GComboBox.DescriptionProvider - Interface in com.biomatters.geneious.publicapi.components: Any items in the GComboBox may implement this interface, in which case, when the drop-down list is being displayed, this description is displayed in grey text after the standard toString() representation of the item.
GComboBox.EnabledStateProvider - Interface in com.biomatters.geneious.publicapi.components: Any items in the GComboBox may implement this interface, in which case, when the drop-down list is being displayed, disabled items will not be selectable.
GComboBox.IconsProvider - Interface in com.biomatters.geneious.publicapi.components: Any items in the GComboBox may implement this interface, in which case they may have an icon rendered next to them.
GDialog - Class in com.biomatters.geneious.publicapi.components: Same as JDialog except when pack() is called, the dialog is resized to ensure that it is no bigger than the max height and width specified by the maxDimensions and no smaller than 300 by 125 pixels.
GDialog(Frame, String, Dimension) - Constructor for class com.biomatters.geneious.publicapi.components.GDialog: See JDialog.JDialog(java.awt.Frame, String)
GDialog(Dialog, String, Dimension) - Constructor for class com.biomatters.geneious.publicapi.components.GDialog: See JDialog.JDialog(java.awt.Dialog, String)
GEditorPane - Class in com.biomatters.geneious.publicapi.components: An implementation of JEditorPane which works around Java bug 6406218 which can result in huge memory leaks.
GEditorPane() - Constructor for class com.biomatters.geneious.publicapi.components.GEditorPane
GEditorPane(URL) - Constructor for class com.biomatters.geneious.publicapi.components.GEditorPane
GEditorPane(String) - Constructor for class com.biomatters.geneious.publicapi.components.GEditorPane
GEditorPane(String, String) - Constructor for class com.biomatters.geneious.publicapi.components.GEditorPane
Geneious - Class in com.biomatters.geneious.publicapi.plugin: General information about the Geneious application.
Geneious() - Constructor for class com.biomatters.geneious.publicapi.plugin.Geneious
Geneious.MajorVersion - Enum in com.biomatters.geneious.publicapi.plugin: Represents a major version number of Geneious (the first 2 numbers of the 3 number version number) for versions of Geneious from 6.0 onwards.
GeneiousAction - Class in com.biomatters.geneious.publicapi.plugin: Geneious action items.
GeneiousAction(String) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousAction
GeneiousAction(String, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousAction
GeneiousAction(String, String, Icons) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousAction
GeneiousAction(String, String, Icons, GeneiousActionOptions.Category, GeneiousActionOptions.MainMenu, boolean, boolean, KeyStroke) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Deprecated.
Construct GeneiousActionOptions first then use constructor GeneiousAction.GeneiousAction(GeneiousActionOptions) instead.
GeneiousAction(GeneiousActionOptions) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Construct a GeneiousAction from GeneiousActionOptions.
GeneiousAction(GeneiousAction) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Creates a GeneiousAction that wraps another action.
GeneiousAction.Divider - Class in com.biomatters.geneious.publicapi.plugin: A subclass of GeneiousAction which is placed in a toolbar/menu as a divider.
GeneiousAction.Divider() - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousAction.Divider
GeneiousAction.SubMenu - Class in com.biomatters.geneious.publicapi.plugin: A subclass of GeneiousAction which is placed in the menu as a submenu which opens to the right; In the toolbar, it will appear as a drop-down menu that opens downwards.
GeneiousAction.SubMenu(GeneiousActionOptions, List<GeneiousAction>) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousAction.SubMenu
GeneiousAction.ToggleAction - Class in com.biomatters.geneious.publicapi.plugin: A subclass of GeneiousAction which is placed in a toolbar/menu as a toggle button or check box menu item.
GeneiousAction.ToggleAction(GeneiousActionOptions) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousAction.ToggleAction: Construct a Toggle action with its properties specified by the GeneiousActionOptions
GeneiousAction.ToggleAction(GeneiousAction.ToggleAction) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousAction.ToggleAction: Creates a ToggleAction that wraps another toggle action.
GeneiousActionOptions - Class in com.biomatters.geneious.publicapi.plugin: Specifies information (such as the name, description,icon, keyboard shortcut and location) of a menu item or button in Geneious.
GeneiousActionOptions(String) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
GeneiousActionOptions(String, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
GeneiousActionOptions(String, String, Icons) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
GeneiousActionOptions(String, String, Icons, GeneiousActionOptions.Category) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Constructor of GeneiousActionOptions for DocumentOperations that belong to a category (eg.
GeneiousActionOptions(String, String, Icons, GeneiousActionOptions.Category, GeneiousActionOptions.MainMenu, boolean, boolean, KeyStroke, boolean) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Deprecated.
Use other constructors in combination with setters instead
GeneiousActionOptions(GeneiousActionOptions) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
GeneiousActionOptions.Category - Enum in com.biomatters.geneious.publicapi.plugin: The category (if any) which this action fits into.
GeneiousActionOptions.MainMenu - Enum in com.biomatters.geneious.publicapi.plugin: All available menu locations.
GeneiousActionOptions.ShortcutChangeListener - Interface in com.biomatters.geneious.publicapi.plugin: A listener that can be notified when the shortcut changes for a GeneiousActionOptions
GeneiousActionToolbar - Class in com.biomatters.geneious.publicapi.components: A panel which contains a JToolbar and adds additional functionality.
GeneiousActionToolbar(Preferences, boolean, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: Construct a GeneiousActionToolbar where the actions will be in the toolbar in the order determined by GeneiousActionOptions.getMainToolbarPosition()/alphabetically for any actions with the same toolbar position value.
GeneiousActionToolbar(Preferences, boolean, boolean, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: Construct a GeneiousActionToolbar
GeneiousActionToolbar.CustomToolbarComponent - Class in com.biomatters.geneious.publicapi.components: Encapsulates the information necessary for adding a custom component to the toolbar.
GeneiousActionToolbar.CustomToolbarComponent(String, JComponent, double, boolean, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar.CustomToolbarComponent: Defines custom toolbar component properties
GeneiousGraphics2D - Interface in com.biomatters.geneious.publicapi.plugin: Provides some (but not all) of the functionality of Graphics2D, but also provides some extra useful methods GeneiousGraphics2D.drawStringWithinBounds(String,int,int,int,int,boolean) GeneiousGraphics2D.drawStringCentred(String, int, int) The primary reason for the existence of this interface is so that SequenceGraphs can be rendered as a circular view in the SequenceViewer correctly.
GeneiousGridDocumentOperation - Class in com.biomatters.geneious.publicapi.plugin: A grid-aware version of DocumentOperation, containing many convenience features to simplify the task of creating a grid-aware DocumentOperation.
GeneiousGridDocumentOperation() - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation
GeneiousGridDocumentOperation.GridInput - Class in com.biomatters.geneious.publicapi.plugin: A class describing all the elements needed to run a program on the grid.
GeneiousGridDocumentOperation.GridInput(List<File>, List<String>, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation.GridInput
GeneiousGridImporter - Class in com.biomatters.geneious.publicapi.plugin: Imports one or more documents into Geneious from the contents of the given folder.
GeneiousGridImporter() - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousGridImporter
GeneiousObjectInputStream - Class in com.biomatters.geneious.publicapi.documents.sequence: An input stream to read from data previously written using a GeneiousObjectOutputStream.
GeneiousObjectInputStream(InputStream) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectInputStream: Constructs a new input stream to read from data previously written using a GeneiousObjectOutputStream.
GeneiousObjectOutputStream - Class in com.biomatters.geneious.publicapi.documents.sequence: An extension to ObjectOutputStream that tries to reduce disk space and also reduce memory usage when the stream is read back in again later.
GeneiousObjectOutputStream(OutputStream, int) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectOutputStream
GeneiousPlugin - Class in com.biomatters.geneious.publicapi.plugin: The base class for all Geneious plugins.
GeneiousPlugin() - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin
GeneiousPreferences - Interface in com.biomatters.geneious.publicapi.plugin: Deprecated.
Use PluginPreferences and GeneiousPlugin.getPluginPreferences() instead
GeneiousPreferences.GeneiousCheckBoxPreference - Class in com.biomatters.geneious.publicapi.plugin: Deprecated.

A preference for specifying a yes/no (on/off) choice.
GeneiousPreferences.GeneiousCheckBoxPreference(String, String, boolean) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousCheckBoxPreference: Deprecated.
GeneiousPreferences.GeneiousComboBoxPreference - Class in com.biomatters.geneious.publicapi.plugin: Deprecated.

A preference for specifying one of a set of values.
GeneiousPreferences.GeneiousComboBoxPreference(String, String, Object[], Object) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousComboBoxPreference: Deprecated.
GeneiousPreferences.GeneiousDependentPreference - Class in com.biomatters.geneious.publicapi.plugin: Deprecated.

A preference which itself contains a list of GeneiousPreferences.GeneiousPreference.
GeneiousPreferences.GeneiousDependentPreference(String, String, GeneiousPreferences.GeneiousPreference[], GeneiousPreferences.GeneiousPreference, List<String>) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousDependentPreference: Deprecated.
GeneiousPreferences.GeneiousPreference - Class in com.biomatters.geneious.publicapi.plugin: Deprecated.

Super class for all GeneiousPreferences.GeneiousPreference types.
GeneiousPreferences.GeneiousRadioButtonPreference - Class in com.biomatters.geneious.publicapi.plugin: Deprecated.

A preference for specifying one of a small set of possible values.
GeneiousPreferences.GeneiousRadioButtonPreference(String, String, String[], String) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousRadioButtonPreference: Deprecated.
GeneiousPreferences.GeneiousStringPreference - Class in com.biomatters.geneious.publicapi.plugin: Deprecated.

A preference for specifying a string.
GeneiousPreferences.GeneiousStringPreference(String, String, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousStringPreference: Deprecated.
GeneiousService - Class in com.biomatters.geneious.publicapi.plugin: A service provides a piece of functionality for the Geneious system.
GeneiousService() - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousService
GeneiousService.ServiceStatus - Enum in com.biomatters.geneious.publicapi.plugin: Possible states of service.
GeneiousServiceListener - Interface in com.biomatters.geneious.publicapi.plugin: Callback used in GeneiousService::initialize to enable a service to report the addition & removal of sub/child-services, and report back a change of status or name.
GeneiousServiceWithPanel - Class in com.biomatters.geneious.publicapi.plugin: This is a GeneiousService that displays a custom panel in Geneious when the service is selected.
GeneiousServiceWithPanel() - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousServiceWithPanel
GeneralUtilities - Class in com.biomatters.geneious.publicapi.utilities: Provides general utility methods that don't fall under any of the other utility classes: FileUtilities, GuiUtilities, StringUtilities, SystemUtilities, ThreadUtilities
generate(AnnotatedPluginDocument[], SequenceAnnotationGenerator.SelectionRange, ProgressListener, Options) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: Create annotations (and/or deletes annotations and/or modifies residues and/or modifies field values) on a set of documents.
generate(PluginDocument, SequenceAnnotationGenerator.SelectionRange, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SingleSequenceResultGenerator: Generate annotations for a single sequence.
generateAnnotations(AnnotatedPluginDocument[], SequenceAnnotationGenerator.SelectionRange, ProgressListener, Options) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: Deprecated.
use generate instead.
Create annotations from a set of documents.
Note: The operation will be run in a non AWT thread. If you need to perform user interface interaction in addition to the options provided in the Options (for example prompting for user input) then you need to place this inside a ThreadUtilities.invokeAndWait() function call.
WARNING: Geneious may call this method multiple times simultaneously. Therefore, any implementation should not store its internal state within instance fields.
WARNING: The default implementation of this method calls SequenceAnnotationGenerator.generate(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange, jebl.util.ProgressListener, Options) but returns only the list of annotations, so any tracks, residue additions or deletions, and annotation deletions will not be respected. If you are invoking a SequenceAnnotationGenerator in another plugin, call SequenceAnnotationGenerator.generate(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange, jebl.util.ProgressListener, Options) instead.
generateAnnotations(SequenceAnnotationGenerator.SelectionRange, ProgressListener, Options, AnnotatedPluginDocument...) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: A convenience method for calling SequenceAnnotationGenerator.generateAnnotations(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange, jebl.util.ProgressListener, Options)
generateAnnotations(SequenceAnnotationGenerator.SelectionRange, ProgressListener, Options, List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: A convenience method for calling SequenceAnnotationGenerator.generateAnnotations(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange, jebl.util.ProgressListener, Options)
generateConsensus(SequenceAlignmentDocument, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Generates a consensus sequence for an alignment using default consensus settings.
generateConsensusSequence(SequenceAlignmentDocument, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Deprecated.
use SequenceUtilities.generateConsensus(com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument, jebl.util.ProgressListener) instead
generateOnAlignments(AnnotatedPluginDocument[], ProgressListener, Options) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: Create annotations (and/or deletes annotations and/or modifies residues and/or modifies field values) on a set of alignments.
generateUniqueLocalURN() - Static method in class com.biomatters.geneious.publicapi.documents.URN: Generates a local unique URN with an URN.assigner of ".".
generateUniqueLocalURN(String) - Static method in class com.biomatters.geneious.publicapi.documents.URN: Generates a unique URN
generateValidValue(DocumentSelectionOption.FolderOrDocuments) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption
generateValidValue(ValueType) - Method in class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption
generateValidValue(Date) - Method in class com.biomatters.geneious.publicapi.plugin.Options.DateOption
generateValidValue(Double) - Method in class com.biomatters.geneious.publicapi.plugin.Options.DoubleOption: Clamps the value to the permissible range.
generateValidValue(Integer) - Method in class com.biomatters.geneious.publicapi.plugin.Options.IntegerOption: Clamps the value to the permissible range.
generateValidValue(ValueType) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Converts a potentially invalid value into a valid one.
generateValidValue(ValueType) - Method in class com.biomatters.geneious.publicapi.plugin.Options.RadioOption
GENETIC_CODE_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Visible, editable field representing a sequence's genetic code.
GENETIC_CODE_NAME - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Name to use for SequenceAnnotationQualifiers that specify a genetic code
GENOME_SEQUENCE_THRESHOLD - Static variable in interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument: The sequence length threshold at which we decide a sequence is a genome.
get() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ExternalSort: Gets the next sorted element
get(int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResultsOnSingleSequence
get(int) - Method in class com.biomatters.geneious.publicapi.utilities.ConcatenatedList
get(int) - Method in class com.biomatters.geneious.publicapi.utilities.IntList.Array
get(int) - Method in class com.biomatters.geneious.publicapi.utilities.IntList: Gets the value at this index.
getAbstract() - Method in interface com.biomatters.geneious.publicapi.documents.types.PublicationDocument: Publication abstract.
getActionOptions() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentAction: Get options for action.
getActionOptions() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: GeneiousActionOptions contains all the important status information including name, description, icon, where the action is displayed in the interface etc.
getActionOptions() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
getActionOptions() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: GeneiousActionOptions contains all the important status information including name, description, icon, where the action is displayed in the interface etc.
getActionProvider() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer: Provide support for this DocumentViewer interacting with copy/paste etc, or any custom actions.
getActions() - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: Get all the GeneiousActions that are in this toolbar.
getActionsAlwaysEnabled() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: a list of Geneious Actions which can appear in the menu bar, toolbar or popup-menu in the service tree.
getActionsEnabledWhenServiceSelected() - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService
getActionsEnabledWhenServiceSelected() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: WritableDatabaseService implements this as a final method to add any additional actions supplied to WritableDatabaseService.addAdditionalAction(com.biomatters.geneious.publicapi.plugin.GeneiousAction) combined with the actions provided by sub-classes in WritableDatabaseService._getActionsEnabledWhenServiceSelected().
getActionsEnabledWhenServiceSelected() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: List of Geneious Actions which can appear in the menu bar, toolbar or popup-menu in the service tree.
getActionsInMainMenuOrder(List<GeneiousAction>) - Static method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Get a sorted list of actions in the order determined by GeneiousActionOptions.getMainMenuPosition()/alphabetically for any actions with the same main menu position value.
getActionsInPopupMenuOrder(List<GeneiousAction>) - Static method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Get a sorted list of actions in the order determined by GeneiousActionOptions.getPopupMenuPosition()/alphabetically for any actions with the same popup menu position value.
getActionsInToolbarOrder(List<GeneiousAction>) - Static method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Get a sorted list of actions in the order determined by GeneiousActionOptions.getMainToolbarPosition()/alphabetically for any actions with the same toolbar position value.
getActiveGeneiousPlugins() - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities
getActiveOptions() - Method in class com.biomatters.geneious.publicapi.plugin.PluginPreferences: Get the option values that should be used by any code that wishes to depend on these options.
getActiveOutputDocuments() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getAddDatabaseOptions(DatabaseService.SequenceSearchQueryType) - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService: Optionally override to return Options which will be displayed to the user (in addition to the standard options) before adding a sequence database.
getAdditionalOptions() - Method in class com.biomatters.geneious.publicapi.plugin.Findable.FindOptions: Get additional options originally provided using Findable.getAdditionalOptions(java.util.concurrent.Callable)
getAdditionalOptions(Callable<String>) - Method in class com.biomatters.geneious.publicapi.plugin.Findable: A sub-class can optionally override this to replace the standard isCaseSensitive with some custom options.
getAdditionalParentDocuments() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getAdditionalPerDocumentXml(AnnotatedPluginDocument, String, boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Get some additional XML associated with a particular document that has been saved using WritableDatabaseService.saveAdditionalPerDocumentXml(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, String, boolean, org.jdom.Element, jebl.util.ProgressListener).
getAdditionalPerDocumentXml(AnnotatedPluginDocument, List<String>, boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Get some additional XML associated with a particular document that has been saved using WritableDatabaseService.saveAdditionalPerDocumentXml(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, String, boolean, org.jdom.Element, jebl.util.ProgressListener) or WritableDatabaseService.saveAdditionalPerDocumentXml(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, boolean, java.util.Map, jebl.util.ProgressListener)
This method is similar to WritableDatabaseService.getAdditionalPerDocumentXml(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, String, boolean, jebl.util.ProgressListener) except that this method allows retrieving multiple additional XML entries with a single method invocation, potentially allowing the database to handle it more efficiently than multiple calls to WritableDatabaseService.getAdditionalPerDocumentXml(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, java.util.List, boolean, jebl.util.ProgressListener)
getAdditionalPerDocumentXmlKeys(boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Get a list of all keys that additional XML has been stored under on any document.
getAdditionalXml(String, boolean) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get additional data in the form of XML which has been stored associated with this document using AnnotatedPluginDocument.setAdditionalXml(String,boolean,org.jdom.Element).
getAdditionalXml(List<String>, boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get additional data in the form of XML which has been stored associated with this document using AnnotatedPluginDocument.setAdditionalXml(java.util.Map, boolean, jebl.util.ProgressListener) or AnnotatedPluginDocument.setAdditionalXml(String, boolean, org.jdom.Element).
getAdvancedPanel() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Get a graphical panel used to display advanced options.
getAffiliation() - Method in interface com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument: Affiliation of the authors of this journal article.
getAffirmativeButton() - Method in class com.biomatters.geneious.publicapi.components.DialogButtonPanel: Get the affirmative button.
getAlignmentDataForSequencesNotInMemory() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: If this document has its non-reference sequences stored as a SequenceListOnDisk, then this returns them along with data associated with them, or null if not.
getAlignmentDocument() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument: Get the alignment document contained within this document
getAlignmentNumberOfColumns() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: If this summary is for an alignment, returns the number of columns in the alignment
getAlignmentOperation(String, SequenceDocument.Alphabet) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get a DocumentOperation representation of an AlignmentOperation.
getAlignmentOperations() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: A AlignmentOperation takes two or more existing sequences and aligns them.
getAlignmentOptionsDescription(List<CharSequence>, Options) - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation: Deprecated.
this functionality is now supplied by operation history
getAlignmentPairwiseSimilarity(boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Get the pairwise similarity if this summary is for an alignment
getAlignments() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentListDocument
getAlignmentSequenceType() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature
getAllButtons() - Method in class com.biomatters.geneious.publicapi.components.DialogButtonPanel: Get all the buttons in this panel in the order they are displayed in the panel on the current platform (left to right).
getAllDisplayableFields() - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Gets a list of all the displayable fields on any document in the user's database
getAllDocumentsUsedWhenNothingSelected() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption: Get whether all documents of the given type are used when nothing is selected.
getAllNotes() - Method in interface com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.DocumentNotes
getAllNoteTypes() - Static method in class com.biomatters.geneious.publicapi.documents.DocumentNoteUtilities: This includes all the users custom note types.
getAlphabet() - Method in enum com.biomatters.geneious.publicapi.databaseservice.DatabaseService.SequenceSearchQueryType
getAlphabet() - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation.InputProperties
getAlphabet() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever: Get the alphabet of the sequence(s)
getAlphabet(SequenceType) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Gets a Geneious alphabet type that is equivalent to a jebl library SequenceType.
getAlphabet(SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Get the Alphabet of a sequence.
getAminoAcidSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
getAminoAcidSequences() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.SequenceListDocument: Gets the amino acid sequences in this document.
getAminoAcidSequences() - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument
getAnnotatedPluginDocument(int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Get the current AnnotatedPluginDocument of one of the sequences being viewed.
getAnnotatedPluginDocumentsForAminoAcidSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: When a SequneceList is created for some existing sequences wrapped in AnnotatedPluginDocument, then the original AnnotatedPluginDocuments are stored in the sequence list.
getAnnotatedPluginDocumentsForNucleotideSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: When a SequneceList is created for some existing sequences wrapped in AnnotatedPluginDocument, then the original AnnotatedPluginDocuments are stored in the sequence list.
getAnnotatedPluginDocumentThatContains(PluginDocument) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Gets the AnnotatedPluginDocument that contains the given PluginDocument.
getAnnotation() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection: Get the selected annotation if there is one
getAnnotationAdjustedForDeletion(int, int, boolean, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Handles a deletion from the sequence which this annotation is for, by either returning a new annotation adjusted to take the deletion into account, or this annotation if it doesn't change, or null if the annotation should be deleted (for example the user deletes nucleotides from a primer annotation)
getAnnotationAdjustedForInsertion(int, int, boolean, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Handles an insertion into the sequence which this annotation is for, by either returning a new annotation adjusted to take the insertion into account, or this annotation if it doesn't change, or null if the annotation should be deleted (for example the user inserts nucleotides into a primer annotation)
getAnnotationAdjustedForReplacement(int, int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Handles a non-gap replacement in the sequence which this annotation is for, by either returning this annotation if it doesn't change, or null if the annotation should be deleted (for example the user replaces nucleotides in a primer annotation)
getAnnotationColoringQualifier() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Returns the name of a qualifier on each annotation in this track whose numeric value is used for determining the intensity of the color of that annotation is rendered in.
getAnnotationColoringQualifierColors() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Gets the color map set by SequenceTrack.setAnnotationColoringQualifierColors(java.util.Map)
getAnnotationGroup(String) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup: Get the annotation group that contains this annotation type
getAnnotationGroups() - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup: Get all available annotation groups
getAnnotationQualifiersToShowAfterNameForRealTimeAnnotations(Options) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: If this is a real time annotation generator (i.e.
getAnnotationSequenceIndex() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection: Get the sequence index of the selected annotation if there is an annotation
getAnnotationsOfType(List<SequenceAnnotation>, String) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Get all annotations in list matching the given type
getAnnotationsOfType(SequenceDocument, String) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Deprecated.
use SequenceUtilities.getAnnotationsOfType(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, String, boolean) instead.
getAnnotationsOfType(SequenceDocument, String, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Get all annotations in document matching the given type.
WARNING: this list may not include all SequenceAnnotations represented as annotations in the sequence viewer.
getAnnotationsOnConsensus() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Gets annotations that are associated with the consensus sequence.
getAnnotationsOnConsensus() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getAnnotationsOnConsensus() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getAnnotationsRevisionNumber() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Gets a revision number associated with the annotations.
getAnnotationsToAdd() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Get the annotations to be added to this sequence.
getAnnotationsToRemove() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Get the annotations to be removed from this sequence.
getAnnotationTypes() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup: Get all of the annotations types contained within this group
getAnnotationTypes() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Gets a set consisting of each annotation type that is present in at least 1 of the sequences.
getApiVersion() - Static method in class com.biomatters.geneious.publicapi.plugin.Geneious: Current Geneious public API version (convenience function) Of the form x.y where x,y are integers.
getApproximateCalculationWorkRequiredPerResidue() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Estimate an amount of work required to calculate graph values per residue.
getArguments() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation.GridInput
getAssemblers() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: A Assembler takes two or more existing sequences and assembles them.
getAssemblers() - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get a list of all Assemblers provided by all currently installed plugins.
getAssignerForCreatingUrn() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService
getAuthors() - Method in interface com.biomatters.geneious.publicapi.documents.types.PublicationDocument: Publication authors.
getAuthors() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: A list of the authors of this module.
getAuthorsString(List<Author>) - Static method in class com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument.Utils: List of authors to nice human readable string.
getAvailableMemory() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities: Get the amount of available (free) memory in bytes.
getAvailableMemoryAfterMostRecentGarbageCollection() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities: Similar to SystemUtilities.getAvailableMemory() but returns the amount of available (free) memory in bytes after the Java virtual machine last performed a garbage collection.
getBackAction() - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: Provide an optional back action that is displayed as a back arrow in the viewer toolbar and has the default back keyboard shortcut.
getBaseElement() - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: A JDOM element holding document data.
getBaseElementString() - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: Base element as a XML text fragment.
getBindingInterval() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Get the interval for the binding region of the oligo sequence (excluding any 5' extension).
getBindingSequence() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Get the sequence of bases making up the binding region of this oligo.
getBitsPerCharIncludingQuality() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getBlastAlignmentText(SequenceAlignmentDocument, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Formats the given alignment in BLAST text format
getBooleanSettingIfNotPresent(String, boolean) - Static method in class com.biomatters.geneious.publicapi.plugin.UserEditablePreferences: Gets a boolean value from user editable preferences, adding an entry if it doesn't already exist.
getBorderInsets(Component) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel.RoundedLineBorder
getBoundsOfMonitorThatRectangleIsMostlyIn(Rectangle) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Find the bounds of the monitor that the majority of the supplied rectangle intersects with and return that monitor's bounds, which excludes the task bar.
getButtonText() - Method in enum com.biomatters.geneious.publicapi.components.Dialogs.SaveChanges: Get the button text that is shown to the user for this option.
getBytes() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ByteBackedCharSequence
getBytesWritten() - Method in class com.biomatters.geneious.publicapi.utilities.OutputStreamThatCountsBytesWritten: Get the number of bytes written so far to this output stream.
getCancelButton() - Method in class com.biomatters.geneious.publicapi.components.DialogButtonPanel: Get the cancel button.
getCancelButton() - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Get the button which is treated as a cancel button.
getCanonicalOrAbsolutePath(File) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Returns the result of calling File.getCanonicalPath(), or if that fails, returns the result of calling File.getAbsolutePath() .
getCategory() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
getCategory() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
getCategoryDefaultIcons(GeneiousActionOptions.Category) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities: Get the default Icons for the specified action category.
getCategoryOperation(GeneiousActionOptions.Category) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get the category operation that includes all other operations in this category.
getCause() - Method in exception com.biomatters.geneious.publicapi.plugin.RuntimeDocumentOperationException
getChainIdentifiers() - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument: Get a collection of the identifiers of all chains in the document
getChainMissingResiduesBefore(String, int) - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument: Number of residues that occur prior to the start of this chain
getCharacterSet() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getCharAndQualityAtIgnoringEndGaps(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Provides both the sequence character and the quality in a single method call, which is almost twice as fast as requesting the 2 values separately.
getCharSequence() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getCharSequence() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument: Get the sequence as a CharSequence.
getCharSequence() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getCharSequence() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
getCharSequence() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
getCharSequenceDataBitOffset() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getCharSequenceRevisionNumber() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Gets a revision number associated with the char sequence.
getCheckBoxLabel() - Method in class com.biomatters.geneious.publicapi.databaseservice.CheckboxSearchOption: Returns the string the search options is labelled with.
getChildOptions() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Get all child options added using Options.addChildOptions(String, String, String, Options).
getChildOptionsPageChooser() - Method in class com.biomatters.geneious.publicapi.plugin.Options: if Options.addChildOptionsPageChooser(String, String, java.util.List, com.biomatters.geneious.publicapi.plugin.Options.PageChooserType, boolean) has been called, return the option created for choosing which set of child options are currently active.
getChildren() - Method in interface com.biomatters.geneious.publicapi.databaseservice.CompoundSearchQuery: Query terms.
getChildService(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Gets a child service whose WritableDatabaseService.getFolderName() == name.
getChildServices() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Provides a list of all the current children of this service.
getChromatogramLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph
getChromatogramLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
getChromatogramLength() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph: The number of points for which this graph has values, which is typically larger than the length of the nucleotide sequence because a base isn't called at every position in the graph.
getChromatogramLength() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideGraphSequenceDocument
getChromatogramLength() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
getChromatogramLength() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
getChromatogramPositionForResidue(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph
getChromatogramPositionForResidue(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
getChromatogramPositionForResidue(int) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph: The graph position (can be used as an argument to NucleotideGraph.getChromatogramValue(int, int)) where the nucleotide at the specified residue index has been called.
getChromatogramPositionForResidue(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideGraphSequenceDocument
getChromatogramPositionForResidue(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
getChromatogramPositionForResidue(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
getChromatogramPositionsForResidues(NucleotideGraph) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Equivalent to calling getChromatogramPositionsForResidues(graph,0,graph.getSequenceLength())
getChromatogramPositionsForResidues(NucleotideGraph, int, int) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Get all the values returned from NucleotideGraph.getChromatogramPositionForResidue(int) for all residues indices in the range startIndex (inclusive) to endIndex (exclusive).
getChromatogramValue(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph
getChromatogramValue(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
getChromatogramValue(int, int) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph: Returns the graph value for the specified nucleotide and at the specified position.
getChromatogramValue(int, int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideGraphSequenceDocument
getChromatogramValue(int, int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
getChromatogramValue(int, int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
getChromatogramValues(NucleotideGraph) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
getChromatogramValues(NucleotideGraph, int) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
getCircularAlignmentLength() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever
getCircularLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: If this alignment is circular, returns the gapped length at which it wraps back to the start or 0 if this alignment is not circular.
getCircularLength() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getClass(String) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Find a class by name in Geneious or in any installed plugin.
getCode() - Method in class com.biomatters.geneious.publicapi.databaseservice.ExtendedSearchOption: Used to get the value in Query.getExtendedOptionValue(String).
getCode() - Method in class com.biomatters.geneious.publicapi.documents.DocumentField: An internal code unique on each document used for identifying this field.
getCode() - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: An internal code unique on each note type used for identifying this field.
getCode() - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType
getCode() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousPreference: Deprecated.

A unique identifier for this preference.
getCodonStart() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: The value of the NCBI_CODON_START qualifier indicates the offset at which the first complete codon of a coding feature can be found, relative to the first base of that feature.
getColor(boolean) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Gets the text/icon color for this folder
getColor(double) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSequenceGraphFactories.SequenceAlignmentScorer: return a Color for a score.
getColor(double) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSequenceGraphFactories.SingleSequenceScorer: return a Color for a score.
getColor() - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics.getColor()
getColumnsWithGapsOverPercentage(double) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: If this summary is for an alignment gets a BitSet indicating which columns contain over the given percentage of gaps.
getComplement(Interval) - Method in class com.biomatters.geneious.publicapi.utilities.Interval
getComplementWithoutReverseSequenceName(String) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Appends the " (complement without reverse)" suffix to the sequence name (or removes if it is already there).
getComponent() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer: Get the graphical component displayed to the user.
getComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions: Get a component used to display these multiple options.
getComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Get a graphical component representing this option.
getComponent() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension
getComponentFillAvailableSpace() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension
getComponentLocation() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension
getComposite() - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D
getCompressedFile(File) - Static method in class com.biomatters.geneious.publicapi.utilities.CompressionUtilities: Returns an instance of CompressionUtilities.CompressedFileWrapper if the specified file contains a single compressed file.
getCondition() - Method in interface com.biomatters.geneious.publicapi.databaseservice.AdvancedSearchQueryTerm: Condition on field.
getCondition() - Method in class com.biomatters.geneious.publicapi.documents.Constraint
getConstraints(Class) - Static method in class com.biomatters.geneious.publicapi.documents.Constraint: Returns an array of conditions which are allowed to be used to constrain the given type.
getConstraints() - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: These are enforced by DocumentNote.setFieldValue(String, Object).
getConstructorAccessorStatic() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getContainingDocument(int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments
getContainingDocumentIndex(List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex: Given a the List of AnnotatedPluginDocument on which this SequenceIndex was defined, returns the index of the document that this SequenceIndex refers to, in that list
getContig() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: If this read represents a contig as input to the assembler, returns that contig.
getContigOutputSupport() - Method in class com.biomatters.geneious.publicapi.plugin.Assembler: Gets the type of data generated by this assembler.
getContigReferenceSequenceIndex() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Get the index (if any) of the reference sequence in a contig.
getContigReferenceSequenceIndex() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getContigReferenceSequenceIndex() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getCopyAction() - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: Action that should be performed when this viewer etc.
getCoverage(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: If this summary is for an alignment, gets the total number of sequences covering this position.
getCoverage(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: If this summary is for an alignment, gets an approximate coverage for the given range.
getCoverageAsDouble(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: If this summary is for an alignment, gets the total number of sequences covering this position.
getCoverageMaximum() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Returns the maximum coverage in this alignment.
getCoverageMaximumAsDouble() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Returns the maximum coverage in this alignment.
getCoverageMean() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Returns the mean coverage in this alignment.
getCoverageStandardDeviation() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Returns the standard deviation of coverage in this alignment.
getCreationDate() - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument
getCreationDate() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get the date this document was created.
getCreationDate() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getCreationDate() - Method in interface com.biomatters.geneious.publicapi.documents.PluginDocument: Get the date this document was created.
getCreationDate() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getCreationDate() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getCreationDate() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
getCreationDate() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
getCreationDate() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getCreationDate() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: This method is not implemented.
getCurrentBackgroundColorFor(char) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Get the current background color for a given residue using the current sequence viewer color scheme.
getCurrentForegroundColorFor(char) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Get the current foreground color for a given residue using the current sequence viewer color scheme.
getCurrentModalDialog() - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Returns the currently active modal dialog shown by Dialogs.
getCurrentThreadCpuTime() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities
getCurrentValue() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousCheckBoxPreference: Deprecated.
getCurrentValue() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousComboBoxPreference: Deprecated.
getCurrentValue() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousRadioButtonPreference: Deprecated.
getCurrentValue() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousStringPreference: Deprecated.
getCursor() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Returns a cursor that will appear when the mouse is over the graph.
getCustomIcon() - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Get the custom icon to use or null if none set
getCustomToolbarComponents() - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: Gets a list of custom components to add to the toolbar displayed at the top of the viewer panel.
getCutAction() - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: Action that should be performed when this viewer etc.
getData(int, int, byte[], byte[], int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Provides sequence character and qualities for multiple positions in a single method call, which is much faster than requesting the values separately.
getDatabase() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get the database folder this document is in, or null if it is not in a database.
getDatabaseFileFormatExtensions() - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService: A list of extensions for file formats that can be added directly to the service.
getDatabaseRoot() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Get the root folder of this database folder hierarchy.
getDatabaseServiceListeners() - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: The default implementations of DatabaseService.addDatabaseServiceListener(DatabaseServiceListener) and DatabaseService.removeDatabaseServiceListener(DatabaseServiceListener) store the listeners in a list that is available for subclasses using this method.
getDatabaseServiceListeners() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Get all DatabaseServiceListeners added using WritableDatabaseService.addDatabaseServiceListener(com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceListener).
getDefaultButton() - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Get the button which is the dialogs default button.
getDefaultComponentLocation() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension
getDefaultExtension() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileExporter: Default extension for file.
getDefaultHeight(int, Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable: If this component does not have a required height (i.e.
getDefaultHeight(int, Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Wrapper
getDefaultHeight() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Supply a default height for this graph.
getDefaultLocale() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities: Returns the real System default locale.
getDefaultLocation() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Determines whether this graph should appear above or below the sequence residues.
getDefaultRenderer(Class<?>) - Method in class com.biomatters.geneious.publicapi.components.GTable
getDefaultShortcut() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
getDefaultSortingField() - Method in class com.biomatters.geneious.publicapi.databaseservice.FolderView: Get the default field on which to sort documents.
getDefaultValue() - Method in class com.biomatters.geneious.publicapi.databaseservice.CheckboxSearchOption: Returns the initial value on opening the search panel.
getDefaultValue() - Method in class com.biomatters.geneious.publicapi.databaseservice.ComboboxSearchOption: Returns the initially selected value in the combo box.
getDefaultValue() - Method in class com.biomatters.geneious.publicapi.databaseservice.TextFieldSearchOption: Initial value on opening the search panel.
getDefaultValue() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Get the default value for this option
getDefaultValues() - Method in class com.biomatters.geneious.publicapi.databaseservice.DependentComboboxSearchOption: Returns a Map of the dependee values to a default value for this combo box when that value is selected in the dependee.
getDefaultVisibility() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Returns whether this graph is visible by default.
getDefaultWidth(Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable: If this component does not have a required width (i.e.
getDefaultWidth(Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Wrapper
getDeleteAction() - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: Action that should be performed when this viewer etc.
getDependeeCode() - Method in class com.biomatters.geneious.publicapi.databaseservice.DependentComboboxSearchOption: Returns the unique identifier of the ComboBoxSearchOption that this depends on.
getDependentChildOptions() - Method in class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption
getDescendantOperationRecords() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument
getDescription() - Method in interface com.biomatters.geneious.publicapi.components.GComboBox.DescriptionProvider: Provide a one line description.
getDescription() - Method in class com.biomatters.geneious.publicapi.databaseservice.ExtendedSearchOption: Gets the description of this option to be displayed as a tooltip.
getDescription() - Method in class com.biomatters.geneious.publicapi.documents.DocumentCollection
getDescription() - Method in class com.biomatters.geneious.publicapi.documents.DocumentField: Returns a one line description of this field.
getDescription() - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNote: Return the descirption of this note type.
getDescription() - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Getter for the document field's description property.
getDescription() - Method in enum com.biomatters.geneious.publicapi.documents.DocumentNoteField.Types: Getter for the description property of this field type.
getDescription() - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType
getDescription() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getDescription() - Method in interface com.biomatters.geneious.publicapi.documents.PluginDocument: A human readable single line of text describing this document, to appear in the description field in the document table.
getDescription() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
getDescription() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getDescription(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Short text description of alignment.
getDescription() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getDescription() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
getDescription() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
getDescription() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
getDescription() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getDescription() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
getDescription() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
getDescription() - Method in class com.biomatters.geneious.publicapi.implementations.structure.DefaultMolecularStructureDocument
getDescription() - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument
getDescription() - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation
getDescription() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory: Description of the viewers purpose and how it is accessed.
getDescription() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
getDescription() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
getDescription() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: A short description of the plugins purpose.
getDescription() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: This gives the human-readable short description of the service as it might appear in any user-interface.
getDescription() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Get a one line description for this option.
getDescription() - Method in class com.biomatters.geneious.publicapi.plugin.Options.OptionValue: get the 1 line description of this option value.
getDescription() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Provides a more verbose description for this graph than SequenceGraph.getName().
getDescriptionAndState() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Describe all properties and the state of these options.
getDescriptionAndState() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Describe all properties and the state of this option.
getDialogHtmlHead() - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Get an HTML <head>...</head> block that should be used for any text pane shown in a dialog.
getDialogOptions() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Returns a Dialogs.DialogOptions to use when laying out a dialog containing your options.
getDirection() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: The direction in which this annotation interval is oriented.
getDisabledLabelForegroundColor() - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Equivalent to calling UIManager.getColor("Label.disabledForeground") except that it returns Color.GRAY if the former would return null
getDisplayableFields() - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument
getDisplayableFields() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get a list of all displayable fields available on the PluginDocument contained within this AnnotatedPluginDocument.
getDisplayableFields() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getDisplayableFields() - Method in interface com.biomatters.geneious.publicapi.documents.PluginDocument: A list of columns for display in the main document panel.
getDisplayableFields() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getDisplayableFields() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getDisplayableFields() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
getDisplayableFields() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
getDisplayableFields() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getDisplayableFields() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
getDisplayableFields() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: This method is not implemented.
getDisplayableFields() - Method in class com.biomatters.geneious.publicapi.implementations.structure.DefaultMolecularStructureDocument
getDisplayableFields() - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument
getDisplayableOptions() - Method in class com.biomatters.geneious.publicapi.plugin.PluginPreferences: Get some options that can be displayed in user preferences.
getDisplayedLabel() - Method in class com.biomatters.geneious.publicapi.plugin.Options.BooleanOption
getDisplayedLabel() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Get a label displayed next to this option.
getDisplayedValue(boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Returns the value with html tags stripped or angle brackets escaped depending on whether html is allowed.
getDocument(URN) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Get a document that exists anywhere within this database (including other folders) with a particular URN.
getDocument() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Returns the underlying document which is wrapped inside this AnnotatedPluginDocument.
getDocumentActions() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: A DocumentAction is similar to a DocumentOperation, but it cannot create new documents.
getDocumentByURN(URN) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Fetches the specified document from either in memory or from the local or a shared database.
getDocumentClass() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get the class of the underlying document without loading it.
getDocumentCount(boolean) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Get the number of documents in this folder
getDocumentFieldCopy() - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField
getDocumentFieldsToSet() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Get all document fields and values added using SequenceAnnotationGenerator.AnnotationGeneratorResult.addDocumentFieldToSet(com.biomatters.geneious.publicapi.documents.DocumentFieldAndValue).
getDocumentFileExporter(String) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: get the DocumentFileExporter with the given unique ID.
getDocumentFileExporters() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: get the exporters provided by this plugin.
getDocumentFileExporters() - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get every DocumentFileExporter provided by any plugin.
getDocumentFileImporter(String) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: get the DocumentFileImporter with the given unique ID.
getDocumentFileImporters() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: get the importers provided by this plugin.
getDocumentFileImporters() - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get every DocumentFileImporter provided by any plugin.
getDocumentHistory() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get the instance of DocumentHistory for this document.
getDocumentLocation(URN) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: If this database contains this document in any user visible folder returns the WritableDatabaseService representing the folder that contains it.
getDocumentName() - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable: Returns the name of the document that we are printing (if applicable)
getDocumentName() - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Wrapper
getDocumentNotes(boolean) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Changes made to the notes on a document will not be saved to the document unless AnnotatedPluginDocument.DocumentNotes.saveNotes() is called after modification.
getDocumentNotesToSet() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Get all notes added using SequenceAnnotationGenerator.AnnotationGeneratorResult.addDocumentNoteToSet(com.biomatters.geneious.publicapi.documents.DocumentNote).
getDocumentOperation(String) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: get the DocumentOperation with the given unique ID.
getDocumentOperations() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: A DocumentOperation takes one or more existing documents and uses them to create a set of new documents.
getDocumentOperations() - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get a list of all DocumentOperations provided by all currently installed plugins.
getDocumentOrCrash() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: A convenience method that calls getDocumentOrThrow(RuntimeException.class).
getDocumentOrNull() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: A convenience method that calls getDocumentOrThrow(true,ProgressListener.EMPTY,...) but instead of throwing an exception if the document cannot be loaded, returns null.
getDocumentOrThrow(boolean, ProgressListener, Class<T>) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Returns the underlying document.
getDocumentOrThrow(Class<T>) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Equivalent to calling getDocumentOrThrow(true,ProgressListener.EMPTY,exceptionClass)
getDocuments() - Method in class com.biomatters.geneious.publicapi.documents.DocumentSearchCache
getDocuments() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.FolderOrDocuments: Get the selected documents or null if documents are not selected (a folder is selected).
getDocuments() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption: Get the list of selected documents.
getDocuments() - Method in exception com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex.SelectionWrongForDocumentsException: Deprecated.
getDocuments() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments
getDocumentSearchCacheFor(DocumentType<T>) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentSearchCache: Gets a cache for the given document type, creating the cache if necessary and caching the cache so that future calls to this method return the same cache.
getDocumentType() - Method in class com.biomatters.geneious.publicapi.documents.DocumentSearchCache
getDocumentTypes() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: get possible document types.
getDocumentTypesForSequenceSearch(DatabaseService.SequenceSearchQueryType, String, Options, boolean) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: Return DocumentSelectionSignatures describing all possible types of documents that can be returned from a sequence search on this service.
getDocumentUrns() - Method in class com.biomatters.geneious.publicapi.databaseservice.FolderView: Get the URNs of all documents for which properties are stored in this folder view.
getDocumentViewerFactories() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: A document viewer displays a set of documents in some graphically interesting way.
getDocumentViewerFactories(AnnotatedPluginDocument...) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get a list of DocumentViewerFactories provided by all currently installed plugins or optionally restrict the returned list to those that can view a given set of documents.
getDocumentVisibleByDefaultOn() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: if this returns a not-null value then this track is only visible by default when viewed from within document with this URN.
getElement(ProgressListener) - Method in interface com.biomatters.geneious.publicapi.documents.ElementProvider: Get an XML element with progress information and the ability to cancel it.
getEmailAddressForCrashes() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: Returns an email address that any crashes that Geneious thinks are likely to be caused by this plugin should be sent to.
getEndGapsManager() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.AlignmentData: Returns an EndGapsManager for these sequences.
getEndGapsManager() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever: If this graph is on an alignment, gets an end gaps manager for quickly finding sequences that intersect a given base number, ignoring end gaps.
getEndPage() - Method in interface com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument: Last page of the article.
getEnumerationValues() - Method in class com.biomatters.geneious.publicapi.documents.DocumentField: The set of possible values for the field.
getEnumerationValues() - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Provides an array of the possible values this field can take.
getExecutableName() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: Returns the name of (or path to) the executable used for local runs (or null if the DocumentOperation does not support local runs)
getExpectedMateDistanceForMate() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Get the expected distance (which may be positive or negative) to find the mate of AssemblerInput.Read.getMate().
getExpectedMateDistanceForRead() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Get the expected distance (which may be positive or negative) to find the mate of AssemblerInput.Read.getRead().
getExpectedMateDistanceNormalized() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Gets the expected distance normalized to be positive.
getExtendedDisplayableFields() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Gets a list of all displayable document fields, which includes all those returned by AnnotatedPluginDocument.getDisplayableFields() as well as the document name, description, creation date and all note fields with DocumentField.getCode()s of the form "noteCode.fieldCode".
getExtendedOptionValue(String) - Method in interface com.biomatters.geneious.publicapi.databaseservice.Query: Get a specialized search option value.
getExtendedPrintable() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer: Get an ExtendedPrintable for providing advanced printing and saving to image support.
getExtendedPrintable() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousServiceWithPanel: You may optionally return an ExtendedPrintable to print the content displayed on the panel.
getExtendedPrintable() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension: Returns an ExtendedPrintable which describes how this extension should be printed.
getExtendedPrintableForTextComponent(JTextComponent) - Static method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Factory: Deprecated.
use ExtendedPrintable.Factory.createExtendedPrintable(javax.swing.JComponent) instead
getExtendedSearchOptions(boolean) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: Provide a list of extended options to be displayed the in the search panel.
getExtendedSearchOptions(boolean) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Provide a list of extended options to be displayed the in the search panel.
getExtensionInterval() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Get the interval for the 5' extension region of the oligo sequence .
getExtensionSequence() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Get the sequence of bases making up the 5' extension region of this oligo.
getExternalActions() - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: Get a list of actions that should appear in the main menu or elsewhere outside the viewer's toolbar.
getExtractionName(String, String, String, boolean) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Create a name for an extracted region
getExtraPersistentInformation() - Method in class com.biomatters.geneious.publicapi.plugin.Options.EditableComboBoxOption
getExtraPersistentInformation() - Method in class com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption
getExtraPersistentInformation() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Gets any information in addition to the option value that should be persistent between instances.
getField() - Method in interface com.biomatters.geneious.publicapi.databaseservice.AdvancedSearchQueryTerm: Field to search in.
getField() - Method in class com.biomatters.geneious.publicapi.documents.DocumentFieldAndValue
getField(String) - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType
getFieldCode() - Method in class com.biomatters.geneious.publicapi.documents.DocumentHistoryEntryField
getFieldName() - Method in class com.biomatters.geneious.publicapi.documents.DocumentHistoryEntryField
getFields() - Method in class com.biomatters.geneious.publicapi.documents.DocumentHistoryEntry
getFields() - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNote: Return all the fields of this note type.
getFields() - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType
getFieldValue(String) - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument
getFieldValue(String) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Retrieves the value of a displayable or hidden field, given the field's code.
getFieldValue(DocumentField) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get value of a field - either a displayable field or a hidden field.
getFieldValue() - Method in class com.biomatters.geneious.publicapi.documents.DocumentHistoryEntryField
getFieldValue(String) - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNote: Returns the value of a particular field given the field code.
getFieldValue(String) - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getFieldValue(String) - Method in interface com.biomatters.geneious.publicapi.documents.PluginDocument: Get the value of a particular field.
getFieldValue(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getFieldValue(Element) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Restore value stored in element by XMLSerializer.fieldValueToElement(String, Object).
getFieldValue(String) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getFieldValue(String) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
getFieldValue(String) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
getFieldValue(String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getFieldValue(String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
getFieldValue(String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: This method is not implemented.
getFieldValueCodes() - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: Gets the code of all fields stored in this document, including non-displayable fields.
getFile() - Method in class com.biomatters.geneious.publicapi.utilities.CompressionUtilities.CompressedFileWrapper
getFileNameExtension(File) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Get the extension of a file name.
getFileNameWithoutExtension(File) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Get the name of a file, excluding its path, excluding its extension and excluding the '.' prior to its extension.
getFileOrFolderSize(File, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: If file is not a directory this returns File.length(), if file is a directory this recurses through all files in the directory and sub directories to return the sum of File.length()s.
getFiles() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation.GridInput
getFileTypeDescription() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileExporter
getFileTypeDescription() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter
getFindable() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer: Provide support for this DocumentViewer to interact with the find text dialog
getFirstName() - Method in class com.biomatters.geneious.publicapi.documents.Author: Returns the first name of the author.
getFirstResidueToReplaceInclusive() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment: Get the 0-based first residue to replace or delete.
getFirstSelectedResidue() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange
getFirstSelectedSequence() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange
getFirstTextComponent(Container) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Gets the first text component in this container.
getFirstUncompressedCharacters(int) - Method in class com.biomatters.geneious.publicapi.utilities.CompressionUtilities.CompressedFileWrapper: Gets the first uncompressed characters of the file.
getFitToScreenZoomLevel() - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel
getFolder() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.FolderOrDocuments: Get the selected folder or null if a folder was not selected (documents are selected).
getFolderName() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Get the name of this DatabaseService folder displayed to the user.
getFolderView() - Method in interface com.biomatters.geneious.publicapi.databaseservice.FolderViewDocument: Get the folder view for this document.
getFolderViewDocument() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: If this folder represents the results of a search, it must provide a FolderViewDocument which stores all properties of that search.
getFont() - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics.getFont()
getForwardAction() - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: Provide an optional forward action that is displayed as a forward arrow in the viewer toolbar and has the default forward keyboard shortcut.
getForwardRegexForSequence(CharSequence, SequenceType, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Equivalent to calling getForwardRegexForSequence(charSequence, sequenceType, interpretAmbiguities, false, true)
getForwardRegexForSequence(CharSequence, SequenceType, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Deprecated.
use SequenceUtilities.getForwardRegexForSequence(CharSequence, jebl.evolution.sequences.SequenceType, boolean, boolean, boolean) instead
getForwardRegexForSequence(CharSequence, SequenceType, boolean, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Given a nucleotide or amino acid sequence, returns a regular expression that matches forward occurrences of this sequence in a larger sequence, i.e.
getForwardRegexPatternForSequence(CharSequence, SequenceType, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Equivalent to calling getForwardRegexPatternForSequence(charSequence, sequenceType, interpretAmbiguities, false)
getForwardRegexPatternForSequence(CharSequence, SequenceType, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Given a nucleotide or amino acid sequence string, returns a regular expression pattern that matches forward occurrences of this search string in a larger sequence string,
getFractionIdenticalSites() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.PairwiseSimilarity
getFractionOfTimeToSaveResults() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter: Returns an approximate fraction of the total operation time which will probably be required to save the imported document(s).
getFractionOfTimeToSaveResults() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: Returns an approximate fraction of the total operation time which will probably be required to save the generated document(s).
getFractionOfTimeToSaveResults() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
getFrame() - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame: Deprecated.
use ProgressFrame.getWindow()
getFrequency(char) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Gets the number of occurrences of the given character
getFrequency() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution.ValueAndFrequency
getFrom() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Start position of annotation.
getFrom() - Method in class com.biomatters.geneious.publicapi.utilities.Interval
getFromResidue() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
getFullPath() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Gives you the full path to this service as it appears in the Geneious service tree.
getGappedIndex(int) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Translates an index in the ungapped sequence to the index of the corresponding nongap character in the gappedSequence passed to the constructor.
getGappedIndex(int, int, boolean, SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Converts an ungapped index to a sequence into the equivalent gapped index.
getGappedSequenceLength() - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation
getGeneiousServerExecutableName() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: If this operation returns true from DocumentOperation.canRunOnGeneiousServer() then this method returns the executable name used to run the operation on the server.
getGeneiousService(String) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get access to any standard GeneiousService or any 3rd party GeneiousService.
getGeneiousServiceListener() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Get the service passed to the GeneiousService.initialize(GeneiousServiceListener) method.
getGeneiousServices() - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Returns all installed GeneiousServices.
getGeneralOptions() - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation: Gets some Options that work for this operation when invoked on any type and number of input sequences
getGeneralOptions() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: Gets some Options that work for this document operation when invoked on any set of input sequences.
getGeneralOptions() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
getGeneralOptions() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation
getGeneralOptions() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: Gets some Options that work for this annotation generator when invoked on any set of input sequences.
getGeneratedAnnotationGroup() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: Get the types of annotations this generator generates.
getGeneticCode(SequenceAnnotation) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities
getGoogleScholarLinkHTML(String, String) - Static method in class com.biomatters.geneious.publicapi.documents.types.PublicationDocument.Utils: Construct a Google Scholar link for a publication
getGraph() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
getGraphAdjustedForDeletion(int, int, SequenceCharSequence) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Returns a new graph equivalent to this one, but adjusted to take into account a deletion from the associated sequence.
getGraphAdjustedForInsertion(int, CharSequence) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Returns a new graph equivalent to this one, but adjusted to take into account an insertion into the associated sequence.
getGraphicsIfFlat() - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D
getGrayedOutIconsOriginal(Icons) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities: Get the non-grayed out version of Icons, IF IconUtilities.createGrayedOutIcons(com.biomatters.geneious.publicapi.plugin.Icons, double, float) was used to create the grayed out version.
getGridInput(AnnotatedPluginDocument[], Options, Options) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: Returns a GeneiousGridDocumentOperation.GridInput object representing all the files and command-line inputs needed to run a job on the grid
getGroupName() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup: Get a name suitable for displaying to an end user describing the annotation types within this group.
getHashSize() - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager: Gets the hash size used for this manager.
getHelp() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: WritableDatabaseService implements this as a final method to add any additional help supplied to WritableDatabaseService.addAdditionalHelp(String) combined with the help provided by sub-classes in WritableDatabaseService._getHelp()
getHelp() - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation
getHelp() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentAction: Help for this action in the form of HTML or plain text.
getHelp() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: Help for this operation in the form of HTML or plain text.
getHelp() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
getHelp() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory: Get help.
getHelp() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: Help for this plugin in the form of HTML or plain text.
getHelp() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Help text.
getHelp() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: Help for this operation in the form of HTML or plain text.
getHelpForFindingProgram() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: Returns an HTML fragment that contains instructions to the user for downloading the program for local runs.
getHiddenElement(String, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: get(load) a special hidden element
getHiddenElementNames() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: lists the hidden elements stored in this database.
getHiddenFolder(String, boolean) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Gets an existing or creates a new hidden folder as an immediate child of the root service of this database.
getHiddenFolderNames() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Get a list of hidden folders that can be used as parameters to the getHiddenFolder() method.
getHistoryEntries() - Method in class com.biomatters.geneious.publicapi.documents.DocumentHistory: Gets the list of entries.
getHtmlHead() - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Get an HTML <head>...</head> block that can be included in displayed HTML pages.
getHtmlStylesheet() - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Get the CSS HTML stylesheet used throughout Geneious when displaying HTML.
getHTMLSummary(Options) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: Should return a summary of the operation that was run including all parameters sent to the command line application and any other options that the user entered.
getIcon() - Method in enum com.biomatters.geneious.publicapi.components.Dialogs.DialogIcon: Get the icon for this DialogIcon
getIcon(int) - Method in class com.biomatters.geneious.publicapi.components.OverlayIcons
getIcon(int) - Method in class com.biomatters.geneious.publicapi.plugin.Icons: Get an icon of size * size dimensions.
getIcon() - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption: Returns the currently set icon, or null if none is set.
getIcon16() - Method in class com.biomatters.geneious.publicapi.components.OverlayIcons
getIcon16() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
getIcon16() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
getIcon16() - Method in class com.biomatters.geneious.publicapi.plugin.Icons: Get a 16 * 16 pixel icon
getIcon24() - Method in class com.biomatters.geneious.publicapi.components.OverlayIcons
getIcon24() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
getIcon24() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
getIcon24() - Method in class com.biomatters.geneious.publicapi.plugin.Icons: Get a 24 * 24 pixel icon
getIcon32() - Method in class com.biomatters.geneious.publicapi.components.OverlayIcons
getIcon32() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
getIcon32() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
getIcon32() - Method in class com.biomatters.geneious.publicapi.plugin.Icons: Get a 32 * 32 pixel icon
getIcons() - Method in interface com.biomatters.geneious.publicapi.components.GComboBox.IconsProvider: Provides the icons for this item.
getIcons() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: WritableDatabaseService implements this as a final method to add any additional icons supplied to WritableDatabaseService.addOverlayIcons(com.biomatters.geneious.publicapi.plugin.Icons) combined with the icons provided by sub-classes in WritableDatabaseService._getIcons()
getIcons() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument
getIcons() - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation
getIcons() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory: An icon which will be displayed (at 16x16) next to the viewer name in the tabbed pane.
getIcons() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
getIcons() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: get plugin icons set.
getIcons() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Icons used in the service list.
getIcons() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Gets Icons associated with these options.
getIcons(String) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities: Create an Icons from an image file on disk.
getIcons(String, String) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities: Create an Icons from two image files on disk: a small and a large version of the image (typically 16x16 pixels and 32x32 (for document icons) or 24x24 (for toolbar icons)).
getIcons() - Method in enum com.biomatters.geneious.publicapi.utilities.StandardIcons: Get the Icons for this standard icon.
getIconsFromJar(Class, String) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities: Create and Icons from an image file in a resource bundle (jar).
getIconsFromJar(Class, String, String) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities: Create and Icons from two image files from a resource bundle (jar).
getIconsName(Icons) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities: Get a string name of an icon for the purposes of lexographic comparison.
getIdentifier() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer.ViewerLocation: Get a short identifier string which is unique for the position of the viewer in the split layout.
getIdentifier() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
getIdentifier() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: This is used so Geneious can identify actions when their name is changed It is simply a concatenation of name and description.
getImage(String) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities: Create an Image from an image file on disk.
getImageFromJar(Class, String) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities: Create and Image from an image file in a resource bundle (jar).
getImmutableGraph() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph.ImmutableGraphProvider: Returns the graph represented as an immutable graph.
getImmutableGraph() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
getImmutablePairedReadManager() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
getImmutablePairedReadManager() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.PairedReads: An immutable view of the paired reads managed by this list or alignment.
getImmutablePairedReadManager() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument
getImmutablePairedReadManager() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getImmutablePairedReadManager() - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Marks this instance as PairedReadManager.setCopyOnWrite() and returns this.
getImporter() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: If this method returns a non-null value, then Geneious will use the returned GeneiousGridImporter to produce documents from the results returned by the operation.
getIncomingMessageHandler() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer: Viewer handling for incoming messages.
getIndexInSequenceListDocument() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument.ReferencedSequence: If SequenceAlignmentDocument.ReferencedSequence.getReferencedDocument() is a SequenceListDocument then this method returns the index of the referenced sequence in that SequenceListDocument
getIndexOfAssemblyReferenceSequenceForContig() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: If this read represents a contig (i.e.
getIndexOfSequenceInDocument() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.ReferenceSequence: If the document returned from AssemblerInput.ReferenceSequence.getSourceAnnotatedPluginDocument() is an alignment or sequence list, this method returns the index of the reference sequence in that document.
getInitials() - Method in class com.biomatters.geneious.publicapi.documents.Author: Returns the initials of the author.
getInputDocuments() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getInputDocumentsArray() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperationInput
getInputDocumentsList() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperationInput
getInputType() - Method in class com.biomatters.geneious.publicapi.databaseservice.TextFieldSearchOption: Returns the type of input expected for this options (text or number etc).
getInt(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getInterlacedExpectedDistance() - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: returns the expected distance (positive) of all reads in this data set if they are all interlaced with a common orientation or 0 if that are not interlaced with a common orientations.
getInterlacedOrientation() - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: returns the orientation of all reads in this data set if they are all interlaced with a common orientation or null if that are not interlaced with a common orientations.
getInternalCharSequence() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getInternalCharSequence() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Returns the CharSequence wrapped by this SequenceCharSequence, representing the sequence without the terminal gaps.
getInternalSequenceLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence
getIntersection(List<List<Interval>>) - Static method in class com.biomatters.geneious.publicapi.utilities.Interval: Returns a (merged) list of the intersecting intervals between groups of annotations.
getIntersectionWith(Interval) - Method in class com.biomatters.geneious.publicapi.utilities.Interval
getInterval() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: If this annotation has exactly 1 interval gets that interval or throws an IllegalStateException if it doesn't have exactly 1 interval.
getIntervals() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Gets all the intervals this annotation contains.
getIntervals() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection: Deprecated.
use SequenceSelection.getIntervals(boolean) instead
getIntervals(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection: Gets the intervals selected
getIntervals() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.SequenceAnnotationWrapper
getIntSettingIfNotPresent(String, int) - Static method in class com.biomatters.geneious.publicapi.plugin.UserEditablePreferences: Gets an integer value from user editable preferences, adding an entry if it doesn't already exist.
getJavaVirtualMachineCpuTime() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities
getJournalTitle() - Method in interface com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument: Non-abbreviated title of the journal that this article is published in.
getKey() - Method in class com.biomatters.geneious.publicapi.plugin.License.PluginLicense
getKeyForPerDocumentPreferencesNeededDuringInitialization() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory: Returns the name of an additional XML key used with PerDocumentPreferences for viewers that need access to the preferences during their swing thread initialization.
getLabel() - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel.RoundedLineBorder: Get the label displayed in the top-left of the border.
getLabel() - Method in class com.biomatters.geneious.publicapi.databaseservice.ExtendedSearchOption: Returns the user visible label.
getLabel() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Get the label display to the user for this option
getLabel() - Method in class com.biomatters.geneious.publicapi.plugin.Options.OptionValue: get the name of this option value displayed to the user.
getLastResidueToReplaceExclusive() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment: Get the 0-based index (exclusive) of the last residue to delete or replace.
getLastSelectedResidue() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange
getLastSelectedSequence() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange
getLeadingGapsLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph
getLeadingGapsLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
getLeadingGapsLength() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.ExtendedNucleotideGraph: Get the number of leading residues in the sequence this graph corresponds to that are all gaps.
getLeadingGapsLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: The number of leading gaps in this SequenceCharSequence, i.e.
getLeadingGapsLength() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
getLeadingGapsLength() - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation
getLeadingGapsLength(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Returns the start index of the non-gap regions in the specified charSequence, i.e.
getLeadingTrimLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Gets the number of bases and non-end gaps at the start of this sequence flagged as trimmed (equivalent to annotations of type SequenceAnnotation.TYPE_TRIMMED).
getLeadingTrimLength(int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever: Get the length (if any) of the leading trimmed region of this sequence
getLegalFileName(String, String) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Get a file name that is guaranteed to be legal by replacing all characters in the given string that are not allowed in a file name with the given replacement.
getLegendName() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Provides an alternative name displayed to the user.
getLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: The length (number of residues and gaps) of this interval.
getLength() - Method in class com.biomatters.geneious.publicapi.utilities.Interval
getLengthOfSequenceIncludingEndGaps() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getLengthOfSequenceIncludingEndGapsStatic() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getLinkAllPairsLayout() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.AlignmentData: Returns an alignment layout where all paired reads are linked.
getLinkNearbyPairsLayout() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.AlignmentData: Returns an alignment layout where nearby paired reads are linked.
getLinkNoPairsLayout() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.AlignmentData: Returns an alignment layout where no paired reads are linked.
getLocationOptions() - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation.InputProperties
getLocationOptions(AnnotatedPluginDocument...) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: Returns Options that can be used to set the location where this operation is run.
getLocationOptions() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperationInput: Gets the location options used to control where the operation is run.
getLocationOptions(Options) - Static method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: A utility method to get the location options (the options visible at the top of the options taken from DocumentOperation.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[]) ) ,
getLocationRelativeToRootPane(Component) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Get the location of the given component relative to the root pane of the component.
getLock() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: An object used as a lock by this database while it modifies the in memory contents of documents.
getMainFrame() - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Get the main Geneious frame (which contains the service tree, document table etc).
getMainMenuLocation() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
getMainMenuLocation() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
getMainMenuPosition() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: The position of the action in the main menu.
getMainToolbarPosition() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: The position of the action in the main toolbar.
getMajorApiVersion() - Static method in class com.biomatters.geneious.publicapi.plugin.Geneious: Major Geneious public API version.
getMajorVersion() - Static method in class com.biomatters.geneious.publicapi.plugin.Geneious
getMasterOptions() - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions: Returns the options that were used to construct this MultipleOptions.
getMate() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Gets the second read in the pair or null if the read in unpaired.
getMateExpectedDistance(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
getMateExpectedDistance(int) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.PairedReads: Gets the expected mate distance (also known as predicted median insert size) of this nucleotide sequence from its mate.
getMateExpectedDistance(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument
getMateExpectedDistance(int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getMateExpectedDistance(int) - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager
getMateIndex(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
getMateIndex(int) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.PairedReads: Gets the index of the mate (if any) of the nucleotide sequence at this index.
getMateIndex(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument
getMateIndex(int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getMateIndex(int) - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager
getMateNormalized() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Gets the second read in the pair or null if the read is unpaired.
getMateNormalizedReversed() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Gets the second read in the pair or null if the read is unpaired normalized such that the 2 reads are forward-reverse orientated.
getMateReferencedDocument() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Gets the referenced document (not the same thing as a reference sequence) for the read returned from AssemblerInput.Read.getMate().
getMateReferencedDocumentNormalized() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Gets the referenced document (not the same thing as a reference sequence) for the read returned from AssemblerInput.Read.getMateNormalized().
getMax() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution
getMax() - Method in class com.biomatters.geneious.publicapi.utilities.Interval: Deprecated.
using Interval.getMaxExclusive() or Interval.getMaxInclusive() instead is recommended as the code is easier to understand and less likely to contain bugs.
getMaxDimensions() - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Get the maximum dimensions that the dialog will pack to.
getMaxExclusive() - Method in class com.biomatters.geneious.publicapi.utilities.Interval
getMaximalAmbiguitySymbol(SequenceType) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: get the code for the state in this sequence type which represents a base/residue that is completely unknown
getMaximumApiVersion() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: Get the maximum major API version number (for example 4) which this plugin is known to work with.
getMaximumCachedUnalignedSequenceLength() - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk: Returns the maximum length of an unaligned sequence which will be cached in memory to improve performance.
getMaximumColumnsCached() - Static method in class com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout: Returns the maximum number of columns in the alignment which will be cached in memory at one time.
getMaximumCoverage() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Coverage
getMaximumCoverageAsDouble() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Coverage
getMaximumHeight(int, Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable: Get the maximum height (inclusive) of the component when saved as an image.
getMaximumHeight(int, Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Wrapper
getMaximumIndex() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: The largest sequence index covered by this interval, equivalent to Math.max(getFrom(), getTo()).
getMaximumNumberOfContigsToGenerate() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput: For performance reasons, the user may limit the algorithm to generating this many contigs.
getMaximumReferenceSequenceLength() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties
getMaximumSequenceLength() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties
getMaximumSequenceLength() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever
getMaximumSequencesCached(boolean) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk: Returns the maximum number of sequences (of length up to if unaligned which will be cached in memory at one time.
getMaximumSize() - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Button
getMaximumSize() - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ToggleButton
getMaximumWidth(Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable: Get the maximum width (inclusive) of the component when saved as an image.
getMaximumWidth(Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Wrapper
getMaxInclusive() - Method in class com.biomatters.geneious.publicapi.utilities.Interval
getMaxResidue() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
getMaxZoomLevel() - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel
getMeanCoverage() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Coverage
getMethod() - Method in class com.biomatters.geneious.publicapi.utilities.CompressionUtilities.CompressedFileWrapper
getMin() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution
getMin() - Method in class com.biomatters.geneious.publicapi.utilities.Interval
getMinimumApiVersion() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: Get the minimum required Geneious API version required for this plugin to operate.
getMinimumCoverage() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Coverage
getMinimumCoverageAsDouble() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Coverage
getMinimumHeight(int, Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable: Get the minimum height (inclusive) of the component when saved as an image.
getMinimumHeight(int, Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Wrapper
getMinimumIndex() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: The smallest sequence index covered by this interval, equivalent to Math.min(getFrom(), getTo()).
getMinimumSequenceLength() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties
getMinimumSize() - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar
getMinimumSuggestedContigSizeForCreatingContigsOnDisk() - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Returns a suggested minimum number of sequences that should be in a SequenceListOnDisk.Builder when creating one.
getMinimumSuggestedReferenceLengthForCreatingContigsOnDisk() - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Returns a suggested minimum sequence length for the reference sequence in a SequenceListOnDisk.Builder when creating one.
getMinimumWidth(Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable: Get the minimum width (inclusive) of the component when saved as an image.
getMinimumWidth(Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Wrapper
getMinorApiVersion() - Static method in class com.biomatters.geneious.publicapi.plugin.Geneious: Minor Geneious public API version.
getMinResidue() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
getMinZoomLevel() - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel
getModifiedDate() - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType: Get the date that this note type was last modified (eg.
getMultipleOptions(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Get a set of multiple options added using Options.addMultipleOptions(String, Options, boolean).
getMultipleOptions() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Get all multiple options added using Options.addMultipleOptions(String, Options, boolean).
getName() - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogAction: Get the name of this action
getName() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Name of document.
getName() - Method in class com.biomatters.geneious.publicapi.documents.DocumentCollection
getName() - Method in class com.biomatters.geneious.publicapi.documents.DocumentField: A nicely formatted one/two words in a human readable form.
getName() - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNote: Return the name of the note type.
getName() - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Getter for the document field's name property.
getName() - Method in enum com.biomatters.geneious.publicapi.documents.DocumentNoteField.Types: Getter for the name property of this field type.
getName() - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType
getName() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getName() - Method in interface com.biomatters.geneious.publicapi.documents.PluginDocument: A short name (preferably one or two words) for the document.
getName() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
getName() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getName() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: The name of the annotation which should be a short human readable text description.
getName() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Get the name of this qualifier.
getName() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getName() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
getName() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
getName() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getName() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
getName() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
getName() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Returns the name of this track.
getName() - Method in class com.biomatters.geneious.publicapi.implementations.structure.DefaultMolecularStructureDocument
getName() - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument
getName() - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation
getName() - Method in class com.biomatters.geneious.publicapi.plugin.Assembler: Provides a short 1 or 2 word name for this algorithm.
getName() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer
getName() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory: Viewer user visible name.
getName() - Static method in class com.biomatters.geneious.publicapi.plugin.Geneious: Application name.
getName() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
getName() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Human readable name for action
getName() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: Name of the plugin suitable for usage in user interface or logs.
getName() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousPreference: Deprecated.

The label displayed next to the input component (eg.
getName() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: This gives the human-readable name of the service as it might appear in any user-interface.
getName() - Method in class com.biomatters.geneious.publicapi.plugin.License.PluginLicense
getName() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Get the name to be used for referencing this option.
getName() - Method in class com.biomatters.geneious.publicapi.plugin.Options.OptionValue: Get the programmatic name used for referencing this option value.
getName() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Provides the name displayed to the user.
getName() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension
getName() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection
getNameDataBitOffset() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getNameInSequenceViewer() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: Specifies whether this annotation generator should appear (and with what name) in the controls on the right-hand side of the sequence viewer and update annotations in real time as the user edits the sequences and/or changes options for this annotation generator.
getNamePatternObject() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getNamesAndValues(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Provides a text description of all option names and values.
getNewResidues() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment: Get the new residues to insert to the residues to replace the existing residues with.
getNewSequence() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment: Gets a new sequence to replace the entire old sequence.
getNext() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange
getNextReadPair() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Reads: Gets the next read or pair of reads.
getNextValue() - Method in class com.biomatters.geneious.publicapi.components.GSpinnerNumberModel: Returns the next number in the sequence.
getNicelyFormattedNameAndValue() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection
getNiceNames(Class) - Static method in class com.biomatters.geneious.publicapi.documents.Constraint: Returns an array of user-friendly names for conditions which are allowed to be used to constrain the given type.
getNoLongerViewedListener() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer: Used to provide notification to the DocumentViewer when the user is no longer interested in viewing it.
getNonZeroLengthIntervals() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection
getNote(String) - Method in interface com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.DocumentNotes
getNoteType(String) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentNoteUtilities: WARNING: These are not defensive copies of the note types so do not modify them unless you are definitely going to call DocumentNoteUtilities.setNoteType(DocumentNoteType) to save them.
getNoteTypeCode() - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNote: Return a unique code for the note type.
getNucleotideGraph(int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever: Get the nucleotide graph (chromatogram) for the sequence at the specified index.
getNucleotideSequenceMaximum() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: get the maximum number of nucleotide sequences this signature accepts, if it is a signature created using forNucleotideSequences() or forNucleotideAndProteinSequences()
getNucleotideSequenceMinimum() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: get the minimum number of nucleotide sequences this signature accepts, if it is a signature created using forNucleotideSequences() or forNucleotideAndProteinSequences()
getNucleotideSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
getNucleotideSequences() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.SequenceListDocument: Gets the nucleotide sequences in this document.
getNucleotideSequences() - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument
getNumberOfAnnotations() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Get the total number of SequenceAnnotations present on the sequences.
getNumberOfAnnotationsOfType(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Get the total number of annotations of the given type present on the sequences.
getNumberOfBitsUsedToStoreLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getNumberOfCharactersExcludingGaps() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: returns the total number of characters (nucleotides or residues) in all the sequences, excluding gaps
getNumberOfCharactersIncludingInternalGaps() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: returns the total number of characters (nucleotides or residues) in all the sequences, including internal gaps, but excluding end gaps.
getNumberOfCircularSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Returns the number of sequences in the list for which SequenceDocument.isCircular() is true
getNumberOfColumns() - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager
getNumberOfColumns() - Method in class com.biomatters.geneious.publicapi.plugin.Options.StringOption: Get the number of columns used for displaying the value of this option.
getNumberOfColumnsInAlignment() - Method in class com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout: Returns the number of columns in the alignment
getNumberOfIdenticalPairs() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.PairwiseSimilarity
getNumberOfIdenticalSites() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.PairwiseSimilarity
getNumberOfImmutableSequenceTrimmedRegions() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Returns the number of trimmed regions in ImmutableSequences.
getNumberOfIntegersOfStorage() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Returns the number of integers needed to store this document on disk and/or load it into memory
getNumberOfMappedLocations() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence
getNumberOfMappedLocations(int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever
getNumberOfMappedLocationsBits() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getNumberOfMappedLocationsDataBitOffset() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getNumberOfNucleotideGraphs() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: returns the number of sequences that are NucleotideGraphs
getNumberOfNucleotideSequences(List<AnnotatedPluginDocument>) - Static method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput: Gets the total number of nucleotide sequences contained in the given documents which may be individual sequences, sequence lists, or alignments/contigs.
getNumberOfNucleotideSequences(AnnotatedPluginDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput: Gets the total number of nucleotide sequences contained in the given document which may be an individual sequence, sequence list, or alignment/contig.
getNumberOfNucleotidesInAllSequences() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties
getNumberOfPairedSequences() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties
getNumberOfPairs() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.PairwiseSimilarity
getNumberOfProcessors() - Static method in class com.biomatters.geneious.publicapi.utilities.MultiThreadedTask
getNumberOfReadSequences() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput
getNumberOfReferenceSequences() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput: Get the total number of reference sequences being assembled to.
getNumberOfReferenceSequences() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties
getNumberOfReversedSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Returns the number of sequences whose name ends with SequenceExtractionUtilities.REVERSED_NAME_SUFFIX
getNumberOfRows() - Method in class com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout: Returns the total number of rows used for laying out sequences
getNumberOfSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout
getNumberOfSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Number of sequences in this alignment
getNumberOfSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Returns the number of sequences added so far to this builder.
getNumberOfSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Returns the number of sequences which this summary is for
getNumberOfSequences() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getNumberOfSequences() - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Get the number of sequences managed by this paired read manger.
getNumberOfSequences() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getNumberOfSequences() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties
getNumberOfSequences() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever: Get the number of sequences.
getNumberOfSequences(List<AnnotatedPluginDocument>, SequenceDocument.Alphabet) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Gets the total number of nucleotide or amino acid sequences contained in the given documents which may be individual sequences, sequence lists, or alignments/contigs.
getNumberOfSequences(AnnotatedPluginDocument, SequenceDocument.Alphabet) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Gets the total number of nucleotide or amino acid sequences contained in the given document which may be an individual sequence, sequence list, or alignment/contig.
getNumberOfSequencesToUseFromDocument(long, double) - Static method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput: When assembling using only a fraction of the data from each document, this is used to return the exact number of sequences used from each document.
getNumberOfSequencesWithAnnotationsOfType(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Get the total number of sequences that have annotations of the given type present.
getNumberOfSequencesWithMates() - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Returns the number of sequences which have mates.
getNumberOfSequencesWithQuality() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: returns the number of sequences that are NucleotideGraphs and return true from NucleotideGraph.hasSequenceQualities()
getNumberOfSequencesWithQuality() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties
getNumberOfSites() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.PairwiseSimilarity
getNumberOfTracks(int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor
getNumberOfTrimmedSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Gets the total number of sequences that either have an annotation of type SequenceAnnotation.TYPE_TRIMMED or have ImmutableSequence.getLeadingTrimLength() or ImmutableSequence.getTrailingTrimLength() greater than 0.
getNumberOfUniqueValues() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution: Get the number of unique values (the number of different values passed to ValueAndFrequencyDistribution.addValue(long, long)
getNumberOfValues() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution: Get the number of values added (the sum of the frequencies passed to ValueAndFrequencyDistribution.addValue(long, long)
getNumericValue() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection
getOligoType() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument
getOperand() - Method in class com.biomatters.geneious.publicapi.documents.Constraint: Returns the operand or value of this constraint (eg.
getOperationId() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getOperator() - Method in interface com.biomatters.geneious.publicapi.databaseservice.CompoundSearchQuery: Query connector.
getOption(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Get an option or child option.
getOptions(SequenceDocument.Alphabet, boolean, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation: Get the options appropriate for aligning these sequences
getOptions(AlignmentOperation.InputProperties) - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation: A more powerful alternative to AlignmentOperation.getOptions(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument.Alphabet, boolean, boolean) that may provide the properties of the input to the operation.
getOptions(OperationLocationOptions, AssemblerInput.Properties) - Method in class com.biomatters.geneious.publicapi.plugin.Assembler: Gets some options to display to the user before performing assembly.
getOptions() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileExporter: Provides all possible options that can be displayed to the user when exporting.
getOptions(AnnotatedPluginDocument[]) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileExporter: Provide some options to display to the user when exporting.
getOptions(List<File>, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter: Provides some options applicable to this importer to the user.
getOptions(AnnotatedPluginDocument...) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: Provides some options applicable to this document operation to the user.
getOptions(SequenceSelection, AnnotatedPluginDocument...) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: More powerful alternative to DocumentOperation.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[]) which may provide the currently selected region of any sequence in the documents.
getOptions(DocumentOperationInput) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: More powerful alternative to DocumentOperation.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[]) which may provide additional values such as the location the operation is run and the currently selected region of any sequence in the documents.
getOptions(List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: A convenience method for calling DocumentOperation.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[])
This method may be invoked from either the swing thread or a non-swing thread.
getOptions(Element, List<AnnotatedPluginDocument>, List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: Recreates some options for rerunning an earlier operation to recreate descendant documents.
getOptions(AnnotatedPluginDocument...) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
getOptions(SequenceSelection, AnnotatedPluginDocument...) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
getOptions(DocumentOperationInput) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
getOptions(Element, List<AnnotatedPluginDocument>, List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
getOptions(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable: Optionally provide additional printing and/or saving image to file options.
getOptions(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Wrapper
getOptions() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
getOptions(DocumentOperationInput) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: Returns options for running the full grid operation (an almagimation of the options given by GeneiousGridDocumentOperation.getProgramOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[]), and some extra options describing where the job will run.
getOptions() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Get a list of all options added via any of the add*Option methods.
getOptions(AnnotatedPluginDocument[], SequenceAnnotationGenerator.SelectionRange) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: Provides some options applicable to this annotation generator to the user.
getOptions(AnnotatedPluginDocument[], SequenceAnnotationGenerator.SelectionRange, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: Similar to SequenceAnnotationGenerator.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange) except that if compactOptions==true then options returned may be more visually compact for rendering in a smaller region, such as in the sequence viewer controls in the case where SequenceAnnotationGenerator.getNameInSequenceViewer() is not null.
getOptions(SequenceAnnotationGenerator.SelectionRange, List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: A convenience method for calling SequenceAnnotationGenerator.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange)
This method may be invoked from either the swing thread or a non-swing thread.
getOptions(SequenceAnnotationGenerator.SelectionRange, AnnotatedPluginDocument...) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: A convenience method for calling SequenceAnnotationGenerator.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange)
This method may be invoked from either the swing thread or a non-swing thread.
getOptions() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Provides options associated with this graph.
getOptionsForBatchExport(AnnotatedPluginDocument[]) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileExporter: Provide some options to display to the user when batch exporting.
getOptionsForRecreatingDescendants() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getOptionsHelp() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Override this method and return a non-null value to have it displayed as html in a dialog when the user clicks on a small help button in the corner of any window showing these options.
getOrderDependentOperationMessage() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: Support for operations caring about the order of similarily typed documents.
getOrderDependentOperationMessage() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
getOrderingRevisionNumber() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
getOrderingRevisionNumber() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceListDocument: Return a revision number that is incremented each time sequences are reordered or removed from this sequence list.
getOriginalIcon() - Method in class com.biomatters.geneious.publicapi.components.OverlayIcons
getOriginalIcon() - Method in class com.biomatters.geneious.publicapi.plugin.Icons: Get the icon used to construct this Icons object if the single parameter constructor was used, or the larger icon if the two parameter constructor was used.
getOtherActions() - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: Get a list of other actions associated with viewer which will be displayed in a toolbar within the viewer panel.
getOtherNames() - Method in class com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument.Taxon: Get any other names that this taxon is known by.
getOutgoingMessageHandler() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer: Get the outgoing message handler.
getOutputDocuments() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getPageCode() - Method in interface com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument: The page code may be S for supplementary or and empty string for standard pages or other codes such as "R".
getPagesRequired(Dimension, Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable
getPagesRequired(Dimension, Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Wrapper
getPagesString() - Method in interface com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument: Article pages in free format.
getPaint() - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics2D.getPaint()
getPairedReadManager() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.AlignmentData: Returns a PairedReadManager for these sequences.
getPanel() - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService
getPanel() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousServiceWithPanel: A panel that is displayed when this service is selected.
getPanel() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Get a graphical panel used to display these options.
getPanel() - Method in class com.biomatters.geneious.publicapi.plugin.TreeViewerExtension: get the panel that appears in the tree viewer controls.
getPanelTitle() - Method in class com.biomatters.geneious.publicapi.plugin.TreeViewerExtension: Get the label that appears above the panel (returned from TreeViewerExtension.getPanel()) in the tree viewer controls.
getParent() - Method in class com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument.Taxon: Get the parent taxon (if any).
getParentDocuments() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getParentOperationRecord() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument
getParentOptions() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: The options of the parent action which represents the submenu this action should appear in.
getParentOptions() - Method in class com.biomatters.geneious.publicapi.plugin.Options
getParentOptions() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Returns the Options in which this option is contained
getParentService() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Get the parent service of this service or null if this service has no parent (it is the root service).
getPasteAction() - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: Action that should be performed when this viewer etc.
getPermissibleExtensions() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter: Standard file name extensions for this document type.
getPluginDocumentXml(ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get the XML of the internal PluginDocument.
getPluginForAssembler(Assembler) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get the GeneiousPlugin that provides a given Assembler via GeneiousPlugin.getAssemblers()
getPluginForDocumentOperation(DocumentOperation) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get the GeneiousPlugin that provides a given DocumentOperation via GeneiousPlugin.getDocumentOperations()
getPluginForSequenceAnnotationGenerator(SequenceAnnotationGenerator) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get the GeneiousPlugin that provides a given SequenceAnnotationGenerator via GeneiousPlugin.getSequenceAnnotationGenerators()
getPluginLicenses() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: Provides a list of all the plugin licenses that are known to be used in this plugin.
getPluginPreferences() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: Get a list of tabs to appear in the Geneious preferences window.
getPopupIcons() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction.SubMenu: Get the icons which should be used for this action when it is displayed as a toolbar button.
getPopupMenuPosition() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: The position of the action in its popup menu.
getPossibleExtensions() - Method in enum com.biomatters.geneious.publicapi.utilities.CompressionUtilities.CompressionMethod
getPossibleExternalActions() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory: Get a list of GeneiousActions for viewer actions that should be displayed in the main menu or other location outside the viewer's toolbar.
getPossibleValues() - Method in class com.biomatters.geneious.publicapi.plugin.Options.BooleanOption
getPossibleValues() - Method in class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption
getPossibleValues() - Method in class com.biomatters.geneious.publicapi.plugin.Options.DoubleOption
getPossibleValues() - Method in class com.biomatters.geneious.publicapi.plugin.Options.EditableComboBoxOption
getPossibleValues() - Method in class com.biomatters.geneious.publicapi.plugin.Options.ExecutableFileSelectionOption
getPossibleValues() - Method in class com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption
getPossibleValues() - Method in class com.biomatters.geneious.publicapi.plugin.Options.IntegerOption
getPossibleValues() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Provide a descriptive string representation of possible values of this option.
getPossibleValues() - Method in class com.biomatters.geneious.publicapi.plugin.Options.RadioOption
getPotentialAdditionalXmlKeys(boolean) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get a list of potential keys for additional xml that is associated with this document.
getPotentialSequencesCoveringArray(int) - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager: Returns all sequences which contain the given index, excluding those sequences for which residueIndex is an end gap, however, the returned list may also include sequences that do not cover the given residueIndex.
getPotentialSequencesCoveringArray(int, int) - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager: Returns all sequences which contain the given index, excluding those sequences for which residueIndex is an end gap, however, the returned list may also include sequences that do not cover the given residueIndex.
getPrecedence() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory: Provide a rough guide about the social status of the viewer.
getPreferences() - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService: Use SequenceDatabaseSuperService.getSetupOptions() instead
getPreferences() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: Deprecated.
GeneiousPreferences are the old style way of providing preferences. Use GeneiousPlugin.getPluginPreferences() instead which is more powerful and more consistent with other areas of the Geneious API.
getPreferences() - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousPreferences: Deprecated.

Get GeneiousPreferences.GeneiousPreferences which will be displayed to the user.
getPreferences() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Deprecated.
use GeneiousPlugin.getPluginPreferences() instead
getPreferencesSuffix() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Returns a preference suffix describing the classes of the current documents being viewed.
getPreviousValue() - Method in class com.biomatters.geneious.publicapi.components.GSpinnerNumberModel: Returns the previous number in the sequence.
getPrimaryDatabaseRoot() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Returns the database root (see WritableDatabaseService.getDatabaseRoot()) for the primary database in this collection.
getPrimaryFileForMultipleFileImporter(List<File>) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter: Determines if this importer supports importing from a list of multiple files.
getPrimerAnnotation() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument
getPrintable() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer: Get a Printable for handling printing and saving as an image If DocumentViewer.getExtendedPrintable() is implemented and returns a non null value, this method will not be used.
getPrintableComponent() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer: Returns the component that Geneious should print (if not the component returned by DocumentViewer.getComponent().
getProbableDataType() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read
getProgramName() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: Returns the name of the program as given on the grid.
getProgramOptions(AnnotatedPluginDocument...) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: This method returns options for running the program
getProgramOptions(Options) - Static method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: A utility method to get the program options (equivalent to options taken from GeneiousGridDocumentOperation.getProgramOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[]) , given options taken from DocumentOperation.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[])
getProgramVersion() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: Returns the version of the program to run on the grid.
getPropertiesForDocument(URN) - Method in class com.biomatters.geneious.publicapi.databaseservice.FolderView: Get the stored properties for a document
getProperty(String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: Returns a value from the internal properties object.
getPropertyFields() - Method in class com.biomatters.geneious.publicapi.databaseservice.FolderView: Get the field definitions for any properties that may appear on documents.
getProteinSequenceMaximum() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: get the maximum number of protein sequences this signature accepts, if it is a signature created using forProteinSequences() or forNucleotideAndProteinSequences()
getProteinSequenceMinimum() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: get the minimum number of protein sequences this signature accepts, if it is a signature created using forProteinSequences() or forNucleotideAndProteinSequences()
getPublicationDate() - Method in interface com.biomatters.geneious.publicapi.documents.types.PublicationDocument: Date of publication.
getPublicationYear() - Method in interface com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument: Year of publication (or -1 if unknown).
getQualifiers() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: A list of qualifiers for the sequence.
getQualifiers() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Returns qualifiers (name/value pairs) associated with this entire track
getQualifiers() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.SequenceAnnotationWrapper
getQualifierValue(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Get the value of the first qualifier in the list of the given name or "" if one is not found.
getQualitiesExcludingGaps() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Returns the distribution of quality values (those returned from NucleotideGraph.getSequenceQuality(int)) across all nucleotides that are non-gaps in all sequences.
getQualitiesExcludingGapsTrimmed() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Returns the distribution of quality values (those returned from NucleotideGraph.getSequenceQuality(int)) across all non-gap non-trimmed nucleotides in all sequences.
getRadioButtons() - Method in class com.biomatters.geneious.publicapi.plugin.Options.RadioOption: Get the list of buttons for this radio option.
getRead() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Gets the first read in the pair or the single read if the read is unpaired.
getReadNormalized() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Gets the first read in the pair or the single read if the read is unpaired.
getReadReferencedDocument() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Gets the referenced document (not the same thing as a reference sequence) for the read returned from AssemblerInput.Read.getRead().
getReadReferencedDocumentNormalized() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Read: Gets the referenced document (not the same thing as a reference sequence) for the read returned from AssemblerInput.Read.getReadNormalized().
getReads() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput
getRealignedName(String) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Given the name of an existing alignment, obtain a name that should be used for a realignment of this alignment.
getRedoAction() - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: Action that should be performed when this viewer etc.
getReferencedAnnotatedDocumentsUrnAndRevisionNumbers() - Method in class com.biomatters.geneious.publicapi.documents.DocumentHistoryEntry: Get the URN and revision numbers of the annotatedPluginDocuments referenced by this entry
getReferencedDocument(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Get an original sequence document that this alignment was made from.
getReferencedDocument() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument.ReferencedSequence: Gets the document a sequence in the alignment was built from.
getReferencedDocument(int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getReferencedDocument(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getReferencedDocuments() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get a set of document URNs referred to by this document.
getReferencedDocuments() - Method in class com.biomatters.geneious.publicapi.documents.DocumentCollection: Any time, either during initial construction of the DocumentCollection, or after this DocumentCollection has been reloaded from the local database, this function can be called to retrieve the list of documents previously remembered using the DocumentCollection.addReferencedDocument(AnnotatedPluginDocument) function.
getReferencedDocuments() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Return the results of SequenceAlignmentDocument.getReferencedDocument(int) for each sequence in the alignment.
getReferencedDocumentUrns() - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: This function can be called to retrieve the list of documents previously remembered using the AbstractPluginDocument.addReferencedDocumentUrn(URN) function.
getReferencedSequence(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Get an original sequence document that this alignment was made from.
getReferencedSequence(int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getReferencedSequence(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getReferencedSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Return the results of SequenceAlignmentDocument.getReferencedSequence(int) for each sequence in the alignment.
getReferenceSequence(int, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput: Gets one of the reference sequences for this assembly.
getReferenceSequenceBases() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary
getReferenceSequenceBasesCovered() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary
getReferenceSequenceIndex() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever: Get the index of the reference sequence in this alignment (if any)
getReferenceSequenceReference(int) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput: Gets a reference to the document that the reference sequence came from.
getReferenceSequences() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Returns the reference sequences currently selected by the user in the options.
getReferenceSequences() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments: If everything in the documents in this SequenceSelection is selected, return a list of the ReferencedSequences representing the AnnotatedPluginDocument which each sequence in the selection appears in and its index therein.
getReferenceSequencesLength() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties
getReferenceSequenceSupport() - Method in class com.biomatters.geneious.publicapi.plugin.Assembler: Gets whether or not this algorithm supports/requires assembling to a reference sequence and if so, whether it can assemble to multiple reference sequences.
getRefinedName(String) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Given the name of an existing alignment, obtain a name that should be used for a refinement of this alignment.
getRenderingHint(RenderingHints.Key) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics2D.getRenderingHint(java.awt.RenderingHints.Key).
getRequiredHeight(int, Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable: Deprecated.
use ExtendedPrintable.getMinimumWidth(Options), ExtendedPrintable.getMaximumWidth(Options) and ExtendedPrintable.getDefaultWidth(Options) instead.
getRequiredHeight(int, Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Wrapper
getRequiredWidth(Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable: Deprecated.
use ExtendedPrintable.getMinimumWidth(Options), ExtendedPrintable.getMaximumWidth(Options) and ExtendedPrintable.getDefaultWidth(Options) instead.
getRequiredWidth(Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Wrapper
getResidueAdjustments() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Get all residue adjustments added using SequenceAnnotationGenerator.AnnotationGeneratorResult.addResidueAdjustment(com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment).
getResidueInterval() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
getResidueIntervals() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange
getResidues(CharSequence, int, boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Gets the residues covered by this interval for displaying to a user.
getResourceForClass(Class, String) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: for grabbing resources based on a directory hirarchy identical to the one that the class cl is found in.
getResultIndex() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResultsOnSingleSequence: returns the index of the only entry in this list which isn't an empty result
getResults() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResultOnAlignment: Gets the results for this alignment.
getResultsDestination() - Static method in class com.biomatters.geneious.publicapi.plugin.ServiceUtilities: Get the service to which results of the current operation will be saved.
getResultsLocation() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperationInput
getResumableState() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback: returns the persistent information that was set with the last call to DocumentOperation.OperationCallback.setResumableState(org.jdom.Element) (this call may have been before the operation was paused)
getResumableState() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback.Wrapper
getReverse() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Returns the reverse of this interval, covering the same sequence residues but having the opposite direction (as defined by SequenceAnnotationInterval.Direction.reverse()).
getReversedSequenceName(String) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Appends the " (reversed)" suffix to the sequence name (or removes if it is already there).
getReverseSort() - Method in class com.biomatters.geneious.publicapi.documents.DocumentField: DocumentField.reverseSort
getRevisionNumber() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get a revision number associated with this document.
getRevisionNumber() - Method in class com.biomatters.geneious.publicapi.documents.UrnWithRevisionNumber
getRootUniqueId() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Get the unique ID for the root folder of this database.
getRowNumber(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout: Get the row number that the given sequence has been lain out in.
getSamePotentialSequencesLowerBound(int) - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager: Gets a lower bound such that all calls to EndGapsManager.getPotentialSequencesCoveringArray(int) with an index between LowerBound and residueIndex inclusive would return the same array.
getSamePotentialSequencesUpperBoundExclusive(int) - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager: Gets an upper bounds such at all calls to EndGapsManager.getPotentialSequencesCoveringArray(int) with an index between residueIndex and this upper bound exclusive would return the same array.
getSaveAction() - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: Provide an optional action which will be performed when the user selects Save from the file menu or pushes Ctrl+S (Cmd+S on Mac OS).
getScaleBarWidth() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Supply a width of the scale bar for this graph.
getScientificName() - Method in class com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument.Taxon: Get the scientific name of this taxon (e.g.
getScore() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getScore(char[], int[]) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSequenceGraphFactories.SequenceAlignmentScorer: Calculates the score for one alignment column based on the residues in each column.
getScore(char) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSequenceGraphFactories.SingleSequenceScorer: return the score for this residue The implementation must be thread safe as this method may be called simulataneously from multiple threads.
getScore(List<CharSequence>, Options) - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation: Used as score parameter when constructing the result alignment, see DefaultAlignmentDocument.DefaultAlignmentDocument(SequenceDocument[], List, String, Double, String)
getSearchableFieldsAndValues() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Equivalent to getSearchableFieldsAndValues(ProgressListener.EMPTY)
getSearchableFieldsAndValues(ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Gets a set of fields and associated values that are indexed for search purposes.
getSearchableFieldsAndValuesForAnnotatedDocumentOnly() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: The same as AnnotatedPluginDocument.getSearchableFieldsAndValues() except that only fields and values for the annotated document are returned.
getSearchContent() - Method in interface com.biomatters.geneious.publicapi.documents.AdditionalSearchContent: List containing search content for geneious to index.
getSearchFields() - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: Gives the set of fields that can be used for searching this repository/database.
getSearchText() - Method in interface com.biomatters.geneious.publicapi.databaseservice.BasicSearchQuery: Get text to search for.
getSelectableValues() - Method in class com.biomatters.geneious.publicapi.plugin.Options.EditableComboBoxOption: return the current selectable values that the option has.
getSelectAllAction() - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: Action that should be performed when this viewer etc.
getSelectedAnnotations() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Gets all currently selected annotations.
getSelectedDocuments() - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Gets the currently selected documents in the Geneious document table.
getSelectedLocation() - Method in class com.biomatters.geneious.publicapi.plugin.OperationLocationOptions
getSelectedSequenceCount() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection: Returns the number of sequences which have any residues selected (0 length selections are included).
getSelectedSequenceIndices() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection
getSelectedSequences() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection: Deprecated.
use SequenceSelection.getSelectedSequenceIndices()
getSelectedService() - Static method in class com.biomatters.geneious.publicapi.plugin.ServiceUtilities: Get the currently selected service in the Geneious service tree on the left-hand side of the main window.
getSelectedServiceOptions(Options) - Static method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: A utility method to get the configuration options for the service this operation has been chosen to run on.
getSelection() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor
getSelectionForAlignmentStatistics() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Returns an adjusted selection suitable for statistics that take alignments into account.
getSelectionForStatistics() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor
getSelectionSignatures() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentAction: Specifies the document(s) this action is available for.
getSelectionSignatures() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileExporter: Specifies the document selections that can be exported.
getSelectionSignatures() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: Specifies the type of documents this operation accepts as input.
getSelectionSignatures() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
getSelectionSignatures() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory: Specifies the type of document(s) viewer can display.
getSelectionSignatures() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: Signatures of set of documents this generator will work on.
getSequence(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Gets one row from the alignment as a SequenceDocument.
getSequence(int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getSequence(int) - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager
getSequence(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getSequence() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval: Deprecated.
use SequenceSelection.SelectionInterval.getSequenceIndex() and SequenceSelection.SequenceIndex.getSequence(java.util.List) instead.
getSequence(List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex: Gets the selected sequence corresponding to this sequence index for these documents
getSequenceAndTrackAnnotations(SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: A convenience method to get all annotations on the sequence and all annotations on all SequenceTracks on this sequence.
getSequenceAnnotation() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.SequenceAnnotationWrapper
getSequenceAnnotationCount() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Returns the number of annotations on this track
getSequenceAnnotationGenerator(String) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: get the SequenceAnnotationGenerator with the given unique ID.
getSequenceAnnotationGenerators() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: A SequenceAnnotationGenerator generates annotations on a sequence, set of sequences, or an alignment.
getSequenceAnnotationGenerators() - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get a list of all SequenceAnnotationGenerators provided by all currently installed plugins
getSequenceAnnotations() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getSequenceAnnotations() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument: Gets sequence annotations which are directly on the sequence.
getSequenceAnnotations() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getSequenceAnnotations() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
getSequenceAnnotations() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
getSequenceAnnotations(ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Gets the annotations for this track, loading them if necessary.
getSequenceAnnotationsIncludingImmutableSequencesTrims(SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Gets all the annotations on the given sequence.
getSequenceAnnotationTypeCount(String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Get the total number of annotations of the given type present in this track
getSequenceAnnotationTypes() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Gets a set consisting of each annotation type that is present at least once on this track
getSequenceAsJeblSequence(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Gets a sequence as a jebl sequence
getSequenceAsJeblSequence(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getSequenceCharSequence(int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever: Get the SequenceCharSequence for the sequence at the specified index.
getSequenceCount() - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager
getSequenceDocument(SequenceDocument.Alphabet) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument.ReferencedSequence: Get the sequence document referenced by this ReferencedSequence (if it references a SequenceDocument or SequenceListDocument)
getSequenceDocument(SequenceAlignmentDocument.ReferencedSequence, SequenceDocument.Alphabet) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument.ReferencedSequence: Get the sequence document referenced by a ReferencedSequence (if it references a SequenceDocument or SequenceListDocument)
getSequenceDocument() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument: Get the sequence document contained within this document
getSequenceDocument(ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.ReferenceSequence: Gets the SequenceDocument corresponding to this reference sequence, loading it from disk if necessary.
getSequenceDocumentType() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
getSequenceDocumentType() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex: returns the type of document the selection applies to.
getSequenceFromPluginDocuments(List<PluginDocument>) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex: Gets the selected sequence corresponding to this sequence index for these documents
getSequenceGapInformation() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Gets SequenceGapInformation associated with the char sequence returned from DefaultSequenceDocument.getCharSequence()
getSequenceGapInformation(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
getSequenceGapInformation(boolean) - Method in interface com.biomatters.geneious.publicapi.implementations.SequenceGapInformation.Provider: Returns a SequenceGapInformation associated with this sequence.
getSequenceGraphFactories() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: A sequence graph displays a graph in the sequence viewer.
getSequenceGraphFactories() - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get a list of all SequenceGraphFactories provided by all currently installed plugins
getSequenceIndex() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval: Returns the sequence index if this is a selection for a single sequence.
getSequenceIndex() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex: Gets the 0-based index of the sequence in the list.
getSequenceIndex() - Method in exception com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex.SelectionWrongForDocumentsException: Deprecated.
getSequenceIndex() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.SequenceAnnotationWrapper
getSequenceIndices() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval: Gets all selected sequence indices.
getSequenceInRowNearestToColumn(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout: For a given row, gets the sequence covering this column index, or if there isn't a sequence covering this column, returns the nearest sequence to it.
getSequenceLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph
getSequenceLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
getSequenceLength() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph: The length of the nucleotide sequence that can be annotated with this graph.
getSequenceLength() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument: Returns the length of the sequence.
getSequenceLength() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getSequenceLength() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
getSequenceLength() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
getSequenceLengthsExcludingGaps() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Gets the distribution of ungapped sequence lengths of all sequences managed by this summary.
getSequenceLengthsExcludingGapsTrimmed() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Gets the distribution of ungapped sequence lengths of all sequences managed by this summary after trim annotations have been applied.
getSequenceList() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Gets the result returned from a previous call to toSequenceList.
getSequenceListSummary() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever: Gets a summary of all the sequences in a sequence list, or all the non-reference sequences in an alignment.
getSequenceName(int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever: Gets the name of the specified sequence.
getSequencePropertyRetriever() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Gets a SequencePropertyRetriever for providing additional information (e.g.
getSequenceQualities(NucleotideGraph) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Equivalent to calling getSequenceQualities(graph,0,graph.getSequenceLength())
getSequenceQualities(NucleotideGraph, int, int) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Get all the values returned from NucleotideGraph.getSequenceQuality(int) for all residues indices in the range startIndex (inclusive) to endIndex (exclusive).
getSequenceQuality(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph
getSequenceQuality(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
getSequenceQuality(int) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph: Returns a measurement of confidence in the residue reported at the specified residueIndex in the sequence.
getSequenceQuality(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideGraphSequenceDocument
getSequenceQuality(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
getSequenceQuality(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
getSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Get the alignment as a list of sequences (Convenience function).
getSequences() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.AlignmentData: Gets the sequences for this data
getSequences() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getSequences() - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager
getSequences() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getSequences() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments: Returns the sequences referred to by this object's SequenceSelection for its List of AnnotatedPluginDocument, as a List of SequenceDocument, applying the given ExtractionStrategy in order to extract sequences.
getSequences(AnnotatedPluginDocument[], SequenceDocument.Alphabet, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: get all the sequences out of a set of AnnotatedPluginDocuments that may wrap SequenceDocuments, SequenceListDocuments or SequenceAlignmentDocuments.
getSequences(List<AnnotatedPluginDocument>, SequenceDocument.Alphabet, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: get all the sequences out of a set of AnnotatedPluginDocuments that may wrap SequenceDocuments, SequenceListDocuments or SequenceAlignmentDocuments.
getSequencesCoveringArray(int) - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager
getSequencesCoveringIterable(int) - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager
getSequencesCoveringIterator(int) - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager
getSequenceSearchOptions(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: Optionally override to provide options which will be displayed at the bottom of the options in the Sequence Search interface when this database is selected and the given program is selected.
getSequenceSearchPrograms(DatabaseService.SequenceSearchQueryType) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: This method can be optionally overridden if this database provides sequence similarity searching and should be available through the Sequence Search interface in Geneious.
getSequenceSelection() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperationInput
getSequenceSelection() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments
getSequencesInAlignmentMaximum() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature
getSequencesInAlignmentMinimum() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature
getSequencesInImmutableList() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Gets an immutable list (whose elements will not change after returning from this method).
getSequencesInImmutableList() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getSequencesInRowIntersectingRange(int, int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout: Gets all sequences in the given row that intersect with the given range of columns
getSequencesRange() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval: Gets the range of sequences selected
getSequenceString() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getSequenceString() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument: Get the sequence as a string.
getSequenceString() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getSequenceString() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
getSequenceString() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
getSequencesWithoutImmediateLoading(AnnotatedPluginDocument[], SequenceDocument.Alphabet) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Like SequenceUtilities.getSequences(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument.Alphabet, jebl.util.ProgressListener) but doesn't require each plugin document to be in memory as long as this Collection is around.
getSequenceTracksToAdd() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Gets the sequence tracks to add to this sequence
getSequenceType() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Returns the sequence type of the first sequence in this alignment (which should be the same as all other sequences in the alignment)
getSequenceType() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getSequenceType() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
getSequenceType() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex
getSequenceType(SequenceDocument.Alphabet) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Gets a jebl library SequenceType that is equivalent to a Geneious alphabet.
getSequenceType(SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Get the (jebl) sequence type.
getSequenceType(AnnotatedPluginDocument) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Examines a document and determines what the (jebl) sequence type (or types) of the document is (or are), and returns it (or them).

Always returns a List<SequenceType> of size 0, 1 or 2.
getSequenceViewerExtensionFactories() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: A SequenceViewerExtension is used for creating a custom extensions to the sequence viewer.
getSequenceViewerExtensionFactories() - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get a list of all SequenceViewerExtension.Factories provided by all currently installed plugins
getServerResource(String) - Static method in class com.biomatters.geneious.publicapi.plugin.Geneious: Gets a resource from the Geneious Server class which is used for resources that we want to make available to a plugin when it is running on the server but we do not to ship it with Geneious
getService(String) - Static method in class com.biomatters.geneious.publicapi.plugin.ServiceUtilities: Calls PluginUtilities.getGeneiousService(String)
getServices() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: A plugin may provides a set of services.
getServiceTreeLabel(boolean, boolean) - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService
getServiceTreeLabel(boolean, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Provide additional details for a human user.
getSetupOptions() - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService: Optionally override to return Options which will be displayed to the user in a services set up section of the interface.
getShortcut() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
getShortcut() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: A keyboard shortcut for the action.
getSignature() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: Get the signature.
getSimilarityFraction() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.PairwiseSimilarity
getSingleSequenceGenerator(Options) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: Optionally provides an alternative way of generating annotations for large data sets to reduce memory usage.
getSize() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get the uncompressed size in bytes of this document
getSizeRequiredToLoadIntoMemory() - Method in interface com.biomatters.geneious.publicapi.documents.PluginDocument.SizeRequiredToLoadIntoMemoryProvider: Return an estimate of the number of bytes required to load this document into memory.
getSizeRequiredToLoadIntoMemory() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
getSizeRequiredToLoadIntoMemory() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getSourceAnnotatedPluginDocument() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.ReferenceSequence: Gets the annotated plugin document that contains this reference sequence.
getStandardDialogFont() - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Get the standard font that is used to render text in dialogs.
getStandardDisplayableField(String) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentField: If fieldCode is for one of the standard fields listed in DocumentField.ALL_STANDARD_FIELDS, then returns that field
getStartPage() - Method in interface com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument: First page of the article.
getStates() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getStatistics(SequenceViewerExtension.PropertyRetrieverAndEditor, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension: Generates one or more sections of statistics to be displayed in the statistics controls section.
getStatus(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Gets the status of this service.
getStdin() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation.GridInput
getStringForKeyStroke(KeyStroke) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Get a string representation for a KeyStroke which can be displayed to the user eg.
getStroke() - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics2D.getStroke()
getStronglyReferencedDocuments() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get a set of document URNs strongly referred to by this document.
getStructure() - Method in interface com.biomatters.geneious.publicapi.documents.types.MolecularStructureDocument: A string representing the molecule structure.
getStructure() - Method in class com.biomatters.geneious.publicapi.implementations.structure.DefaultMolecularStructureDocument
getStyleSheet() - Method in class com.biomatters.geneious.publicapi.components.GTextPane.MemoryFixedHTMLEditorKit
getSubMenuActions() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction.SubMenu: Get the actions that appear in the submen/popup-menu, in the same order they will appear in the menu.
getSubmenuDividerPositions() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: List of positions for dividers if these are parentOptions passed to GeneiousActionOptions.createSubmenuActionOptions(GeneiousActionOptions, GeneiousActionOptions)
getSuggestedTrackNameSuffixForAlignmentWithReferenceSequence(AnnotatedPluginDocument, SequenceAlignmentDocument) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Returns a suggested track name suffix to use for tracks created on an alignment with a reference sequence.
getSummary() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Deprecated.
use AnnotatedPluginDocument.getFieldValue(DocumentField) with DocumentField.DESCRIPTION_FIELD to get the Description for the docment.
getSummary() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Provider: Gets a summary of the properties of the sequences.
getSummary() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getSupportedCharacters(SequenceDocument.Alphabet) - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation: Get the characters that are supported by this alignment operation.
getSurname() - Method in class com.biomatters.geneious.publicapi.documents.Author: Returns the surname of the author.
getTabIcon() - Method in class com.biomatters.geneious.publicapi.plugin.PluginPreferences: Get an icon displayed next to the name returned from PluginPreferences.getTabName().
getTabName() - Method in class com.biomatters.geneious.publicapi.plugin.PluginPreferences: Get the name displayed in the heading of the tab for these options in the preferences pane.
getTabPosition() - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation
getTaxon() - Method in interface com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument: Get the taxon of this document.
getTaxonomicLevel() - Method in class com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument.Taxon: Get the taxonomic level of this taxon (e.g.
getTemporaryFieldValue(String) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: This us used for retrieving temporary in memory only information about this document.
getText() - Method in class com.biomatters.geneious.publicapi.plugin.Findable.FindOptions: Get text to be searched for.
getTextFromFile(File) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Reads the entire contents of a file into a string.
getTextFromInputStream(InputStream, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Reads an InputStream into a string until the end of the stream is reached.
getTextFromReader(Reader, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Reads a reader into a string until the end of the stream is reached.
getTimeAtWhichOperationWasRun() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getTitle() - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Get the desired title for the dialog
getTitle() - Method in interface com.biomatters.geneious.publicapi.documents.types.PublicationDocument: Publication title.
getTo() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: End position of annotation, usually (but not always) in the range 1 to the length of the sequence inclusive.
getTo() - Method in class com.biomatters.geneious.publicapi.utilities.Interval: Deprecated.
using Interval.getToExclusive() ()} or Interval.getToInclusive() ()} instead is recommended as the code is easier to understand and less likely to contain bugs.
getToExclusive() - Method in class com.biomatters.geneious.publicapi.utilities.Interval
getToInclusive() - Method in class com.biomatters.geneious.publicapi.utilities.Interval
getToolbarActions() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension: Get a list of other actions associated with extension which will be displayed in the sequence viewer toolbar.
getToolbarName() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions
getTooltip() - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogAction: Get the tooltip for the button associated with this action
getToResidue() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
getTotalBuildTimes() - Static method in class com.biomatters.geneious.publicapi.utilities.xml.FastSaxBuilder: Get a text description of the total time spent parsing XML by all FastSAXBuilders.
getTotalSelection(List<AnnotatedPluginDocument>, SequenceType, SequenceSelection.SequenceDocumentType) - Static method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection: For a List of AnnotatedPluginDocument, creates a selection that represents a "Select all" on each of the documents.
getTrackColoringQualifiers() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack
getTrackIndex() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.SequenceAnnotationWrapper
getTrackManager(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getTrackManager(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
getTrackManager(SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Gets the track manager (if any) for a sequence.
getTrackManager(SequenceAlignmentDocument) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Gets the track manager (if any) for the consensus sequence of an alignment.
getTrackManager(boolean) - Method in interface com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager.Provider: Gets a SequenceTrack.Manager associated with this sequence for providing sequence tracks.
getTrackName(int, int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor
getTracks() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Gets all tracks on this sequence.
getTrailingGapsLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph
getTrailingGapsLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
getTrailingGapsLength() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.ExtendedNucleotideGraph: Get the number of trailing residues in the sequence this graph corresponds to that are all gaps.
getTrailingGapsLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: The number of trailing gaps in this SequenceCharSequence.
getTrailingGapsLength() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
getTrailingGapsLength() - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation
getTrailingGapsLength(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Get the number of trailing gap ('-') characters in the sequence.
getTrailingGapsStartIndex() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Get the index in the sequence at which the trailing gaps (if any) start.
getTrailingGapsStartIndex() - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation
getTrailingGapsStartIndex(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Returns the end index of the non-gap regions in the specified charSequence.
getTrailingTrimLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Gets the number of bases and non-end gaps at the end of this sequence flagged as trimmed (equivalent to annotations of type SequenceAnnotation.TYPE_TRIMMED)
getTrailingTrimLength(int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever: Get the length (if any) of the traling trimmed region of this sequence
getTranslation(AnnotatedPluginDocument, SequenceDocument, SequenceAnnotation) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Returns the translation (if applicable) for the given annotation.
getTree() - Method in interface com.biomatters.geneious.publicapi.documents.types.RootedTreeDocument: Get the tree.
getTree() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
getTrees() - Method in interface com.biomatters.geneious.publicapi.documents.types.SameTaxaTreesDocument: Get tree set.
getTrees() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
getTrees() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
getTrees() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
getTreeViewerExtensionFactories() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: A TreeViewerExtension is used for creating a custom controls section in the tree viewer.
getTreeViewerExtensionFactories() - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Get a list of all TreeViewerExtension.Factories provided by all currently installed plugins
getTrialLength() - Method in class com.biomatters.geneious.publicapi.plugin.License.PluginLicense
getTrialVersion() - Method in class com.biomatters.geneious.publicapi.plugin.License.PluginLicense
getTrimDataBitOffset() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getType() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Type of the annotation.
getType() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.SequenceAnnotationWrapper
getTypeFor(DocumentNoteField) - Static method in enum com.biomatters.geneious.publicapi.documents.DocumentNoteField.Types: Returns the Types object for this documentNoteField.
getUncompressedInputStream(ProgressListener) - Method in class com.biomatters.geneious.publicapi.utilities.CompressionUtilities.CompressedFileWrapper
getUndoAction() - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: Action that should be performed when this viewer etc.
getUngappedIndexFromExtractedRegion(int, int, boolean, SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Converts a gapped index to a sequence into the equivalent ungapped index, and then further adjusts the index to account for any SequenceAnnotation.TYPE_EXTRACTED_REGION annotation covering the position
This method should either be invoked from the Swing thread, or by an extension that has registered a SequenceViewerExtension.PropertyRetrieverAndEditor.DiscardReferencesCallback and has not been instructed to discard references.
getUngappedIndexOfThisOrNextResidue(int) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Same as SequenceGapInformation.getUngappedIndexOfThisOrPreviousResidue(int), but if the specified index is on a gap in the gapped sequence, then the ungapped index of the next rather than the previous nongap residue is returned.
getUngappedIndexOfThisOrNextResidue(SequenceCharSequence, int) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Gets the ungapped index corresponding to a gapped index.
getUngappedIndexOfThisOrNextResidue(int, int, boolean, SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Converts a gapped index in a sequence into the equivalent ungapped index.
getUngappedIndexOfThisOrNextResidueTreatingEndGapsLikeInternalGaps(int) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Same as SequenceGapInformation.getUngappedIndexOfThisOrPreviousResidueTreatingEndGapsLikeInternalGaps(int), but if the specified index is on a gap in the gapped sequence, then the ungapped index of the next rather than the previous nongap residue is returned.
getUngappedIndexOfThisOrPreviousResidue(int) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Calculates the index where the character gappedSequence.charAt(indexInGappedSequence) would move if all gaps were stripped from gappedSequence.
getUngappedIndexOfThisOrPreviousResidue(SequenceCharSequence, int) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Gets the ungapped index corresponding to a gapped index.
getUngappedIndexOfThisOrPreviousResidue(int, int, boolean, SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Converts a gapped index in a sequence into the equivalent ungapped index.
getUngappedIndexOfThisOrPreviousResidueTreatingEndGapsLikeInternalGaps(int) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Calculates the index where the character gappedSequence.charAt(indexInGappedSequence) would move if all gaps were stripped from gappedSequence.
getUngappedLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getUngappedLength() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: returns the length of this sequence, excluding any gaps (both internal and end gaps)
getUngappedSequenceLength() - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Returns the ungapped length of the sequence passed to the constructor
getUniqueID() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Get a unique ID for this database service.
getUniqueId() - Method in class com.biomatters.geneious.publicapi.plugin.Assembler: Gets a unique id for this algorithm.
getUniqueId() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileExporter: Get a unique identifier for this DocumentFileExporter.
getUniqueId() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter: Get a unique identifier for this DocumentFileImporter.
getUniqueId() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: Get a unique identifier for this DocumentOperation.
getUniqueID() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Get a unique identifier for this GeneiousService.
getUniqueId() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: Get a unique identifier for this SequenceAnnotationGenerator.
getUniqueId() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension
getUniqueId() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsFactory
getUniqueIdPrefix() - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation
getUniqueNameForDocument(String) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Deprecated.
use getUniqueNameForDocument(String, WritableDatabaseService, Collection)
getUniqueNameForDocument(String, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Deprecated.
use getUniqueNameForDocument(String, WritableDatabaseService, Collection)
getUniqueNameForDocument(String, WritableDatabaseService) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Generate a document name that is unique to the given folder, based on the original name passed in.
getUniqueNameForDocument(String, WritableDatabaseService, Collection<String>) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Generate a document name that is unique to the given folder, based on the original name passed in.
getUniqueTrackName(Set<String>, String) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Creates a track name that isn't in a given set of names.
getUniqueTrackName(List<SequenceTrack.Manager>, String) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Creates a name unique among all tracks in all these managers.
getUniqueTrackName(String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Creates a name unique among all tracks in this manager.
getURN() - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument
getURN() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: A unique URN which serves as a primary database key for this document.
getURN() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getURN() - Method in interface com.biomatters.geneious.publicapi.documents.PluginDocument: A Universal Resource Name.
getURN() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
getUrn() - Method in class com.biomatters.geneious.publicapi.documents.UrnWithRevisionNumber
getURN() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getURN() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
getURN() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
getURN() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getURN() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: This method is not implemented.
getUsedMemory() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities: Get the amount of used memory in bytes.
getUserEditablePreferences() - Static method in class com.biomatters.geneious.publicapi.plugin.UserEditablePreferences
getUserMessage() - Method in exception com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceException: Human readable message.
getUserSelectedColor(Color, JComponent, String) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: gets a color selected by the user in a color chooser dialog.
getUserSelectedColor(Color, JComponent, String, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: gets a color selected by the user in a color chooser dialog.
getUserSelectedFile(String, FilenameFilter, int) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Displays a file open dialog to the user (a Java dialog on windows and unix, a Mac dialog on MacOS), and returns the file that the user selected (or null if they cancelled)
getUserSelectedFolder(Component) - Static method in class com.biomatters.geneious.publicapi.plugin.ServiceUtilities: Opens a dialog in which the user can choose one of their local database folders.
getUserSelectedSaveFile(String, String, String, String) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Displays a file save dialog to the user (a Java dialog on windows and unix, a Mac dialog on MacOS), and returns the file that the user selected (or null if they cancelled)
getValidSequence(SequenceDocument, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Replace any invalid bases/residues in the given sequence document with ambiguity symbols.
getValidSequence(SequenceDocument, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Replace any invalid bases/residues in the given sequence document with ambiguity symbols or gaps.
getValue() - Method in class com.biomatters.geneious.publicapi.documents.DocumentFieldAndValue
getValue() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Get the value of this qualifier.
getValue() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution.ValueAndFrequency
getValue(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: get the value of the option with the name optionName.
getValue() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Get the current value of this option.
getValue(int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph
getValueAsString(DocumentSelectionOption.FolderOrDocuments) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption
getValueAsString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Get the value of this option as a string.
getValueAsString(ValueType) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Converts this value to a String suitable for returning from Options.getValueAsString(String).
getValueAsString() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Converts the current value of this option to a String by calling getValueAsString(getValue())
This method is the inverse of Options.Option.getValueFromString(String).
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.BooleanOption
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.DateOption
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.DoubleOption
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.EditableComboBoxOption
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.ExecutableFileSelectionOption
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.IntegerOption
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleLineStringOption
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Convert a String into an instance of the object type used by this option.
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.RadioOption
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.StringOption
getValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionGrabOption
getValues() - Method in interface com.biomatters.geneious.publicapi.databaseservice.AdvancedSearchQueryTerm: Values associated with condition.
getValues() - Method in class com.biomatters.geneious.publicapi.databaseservice.ComboboxSearchOption: Returns a String array containing the values displayed in the combo box.
getValues() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution: Gets a sorted list of values and their frequencies.
getValues() - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions: Get all the current values for a set of multiple options.
getValuesMap() - Method in class com.biomatters.geneious.publicapi.databaseservice.DependentComboboxSearchOption: Returns a Map of the dependee values to the set of values that this combo box should have for each of those values.
getValueType() - Method in class com.biomatters.geneious.publicapi.documents.DocumentField: Returns the class of the value which this field represents.
getValueType() - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Gets the class of the value represented by this field.
getValueType() - Method in enum com.biomatters.geneious.publicapi.documents.DocumentNoteField.Types: Returns the class of the value that this note field represents.
getVersion() - Static method in class com.biomatters.geneious.publicapi.plugin.Geneious: Get the current Geneious version.
getVersion() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: Version number of this plugin.
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.databaseservice.FolderView
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.documents.DocumentCollection
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.documents.DocumentField
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Implements XMLSerializable.OldVersionCompatible#getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType) but note that SequenceCharSequence is guaranteed to be able to always serialize to Geneious.MajorVersion#Version6_0
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.AlignmentData
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution
getVersionSupport(XMLSerializable.VersionSupportType) - Method in interface com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible: Gets either the latest version this class can serialize to via XMLSerializable.OldVersionCompatible.toXML(com.biomatters.geneious.publicapi.plugin.Geneious.MajorVersion, jebl.util.ProgressListener) or the most recent version in which the XML returned from XMLSerializable.OldVersionCompatible.toXML(com.biomatters.geneious.publicapi.plugin.Geneious.MajorVersion, jebl.util.ProgressListener) last changed.
getVersionSupport(XMLSerializable) - Method in enum com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType: Helper method for implementing XMLSerializable.OldVersionCompatible.getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType) that returns that delegates to the given object if it implements OldVersionCompatible or returns Geneious.getMajorVersion() if it doesn't.
getVersionSupport(XMLSerializable.VersionSupportType, Object...) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Helper method for implementing XMLSerializable.OldVersionCompatible.getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType)
Out of all values, returns the highest version of Geneious that any individual value supports serialization to via XMLSerializer.fieldValuesToElement(String, java.util.Map), XMLSerializer.fieldValueToElement(String, Object), XMLSerializer.classToXML(String, XMLSerializable) or XMLSerializer.classToXML(String, XMLSerializable, jebl.util.ProgressListener).
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager: Like XMLSerializable.OldVersionCompatible#getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType) but this class isn't really XML serialiable.
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.EValue
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.Percentage
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.ExtractionStrategy
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments
getVersionSupport(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.utilities.Interval
getVersionSupportForValuesToXML(XMLSerializable.VersionSupportType) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Gets the version support as defined by OldVersionCompatible#getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType) for use with Options.valuesToXML(com.biomatters.geneious.publicapi.plugin.Geneious.MajorVersion, String)
getVersionSupportStatic(XMLSerializable.VersionSupportType) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: A static implementation of SequenceAnnotation.getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType) that can be used in place of that method since all SequenceAnnotation instances have the same version support.
getVersionSupportStatic(XMLSerializable.VersionSupportType) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Returns version support as defined by XMLSerializable.OldVersionCompatible#getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType).
getVerticalPosition() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection
getVerticalWeight() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Get the weighting used to decide how much this component should stretch when its container is resized.
getVisibleAnnotations(SequenceViewerExtension.PropertyRetrieverAndEditor.DiscardReferencesCallback) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Gets all currently visible (after applying the filter) annotations.
getVolume() - Method in interface com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument: The volume of the journal that the article is published in.
getWatermarkText() - Method in class com.biomatters.geneious.publicapi.plugin.Options.StringOption: Returns the string passed into #StringOption(String, String, String, String) (this value may be null)
getWeaklyReferencedDocuments() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Get a set of document URNs weakly referred to by this document.
getWindow() - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame: Get the window which is used to display progress.
getWritableDatabaseServiceRoots() - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Returns the root services of all installed WritableDatabaseServices.
getZoomLevel() - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel
getZoomSlider() - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: Gets a slider that also controls zooming.
GLabel - Class in com.biomatters.geneious.publicapi.components: Same as JLabel except it has the option to use a smaller font.
GLabel(String, Icon, int) - Constructor for class com.biomatters.geneious.publicapi.components.GLabel
GLabel(String, int) - Constructor for class com.biomatters.geneious.publicapi.components.GLabel
GLabel(String, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.GLabel: Calls JLabel.JLabel(String) and optionally uses a font 1pt smaller than the default.
GLabel(String) - Constructor for class com.biomatters.geneious.publicapi.components.GLabel
GLabel(Icon, int) - Constructor for class com.biomatters.geneious.publicapi.components.GLabel
GLabel(Icon) - Constructor for class com.biomatters.geneious.publicapi.components.GLabel
GLabel() - Constructor for class com.biomatters.geneious.publicapi.components.GLabel
GPanel - Class in com.biomatters.geneious.publicapi.components: Same as JPanel except not opaque by default.
GPanel(LayoutManager, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.GPanel
GPanel(LayoutManager) - Constructor for class com.biomatters.geneious.publicapi.components.GPanel
GPanel(boolean) - Constructor for class com.biomatters.geneious.publicapi.components.GPanel
GPanel() - Constructor for class com.biomatters.geneious.publicapi.components.GPanel
GPopupMenu - Class in com.biomatters.geneious.publicapi.components: Has the same functionality as a JPopupMenu but will correctly hide when switching between windows on Mac OS.
GPopupMenu() - Constructor for class com.biomatters.geneious.publicapi.components.GPopupMenu
GPopupMenu(String) - Constructor for class com.biomatters.geneious.publicapi.components.GPopupMenu
GprDocument - Class in com.biomatters.geneious.publicapi.implementations.structure: A Gpr molecular structure document.
GprDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.structure.GprDocument
GSpinnerNumberModel - Class in com.biomatters.geneious.publicapi.components: Just like SpinnerNumberModel but allow reaching the maximum/minimum using up/down controls, rather than stopping at the value before the maximum/minimum
e.g.
GSpinnerNumberModel(Number, Comparable, Comparable, Number) - Constructor for class com.biomatters.geneious.publicapi.components.GSpinnerNumberModel: See SpinnerNumberModel.SpinnerNumberModel(Number, Comparable, Comparable, Number)
GSpinnerNumberModel(int, int, int, int) - Constructor for class com.biomatters.geneious.publicapi.components.GSpinnerNumberModel: See SpinnerNumberModel.SpinnerNumberModel(int, int, int, int)
GSpinnerNumberModel(double, double, double, double) - Constructor for class com.biomatters.geneious.publicapi.components.GSpinnerNumberModel: See SpinnerNumberModel.SpinnerNumberModel(double, double, double, double)
GSpinnerNumberModel() - Constructor for class com.biomatters.geneious.publicapi.components.GSpinnerNumberModel: See SpinnerNumberModel.SpinnerNumberModel()
GTable - Class in com.biomatters.geneious.publicapi.components
GTable() - Constructor for class com.biomatters.geneious.publicapi.components.GTable
GTable(TableModel) - Constructor for class com.biomatters.geneious.publicapi.components.GTable
GTable(TableModel, TableColumnModel) - Constructor for class com.biomatters.geneious.publicapi.components.GTable
GTable(TableModel, TableColumnModel, ListSelectionModel) - Constructor for class com.biomatters.geneious.publicapi.components.GTable
GTable(int, int) - Constructor for class com.biomatters.geneious.publicapi.components.GTable
GTable(Vector, Vector) - Constructor for class com.biomatters.geneious.publicapi.components.GTable
GTable(Object[][], Object[]) - Constructor for class com.biomatters.geneious.publicapi.components.GTable
GTextArea - Class in com.biomatters.geneious.publicapi.components: Same as JTextArea but has undo/redo capability, a popup Edit menu and is linked to the main Edit menu.
GTextArea() - Constructor for class com.biomatters.geneious.publicapi.components.GTextArea: See JTextArea.JTextArea()
GTextArea(String) - Constructor for class com.biomatters.geneious.publicapi.components.GTextArea: See JTextArea.JTextArea(String)
GTextArea(int, int) - Constructor for class com.biomatters.geneious.publicapi.components.GTextArea: See JTextArea.JTextArea(int, int)
GTextArea(String, int, int) - Constructor for class com.biomatters.geneious.publicapi.components.GTextArea: See JTextArea.JTextArea(String, int, int)
GTextArea(Document) - Constructor for class com.biomatters.geneious.publicapi.components.GTextArea: See JTextArea.JTextArea(javax.swing.text.Document)
GTextArea(Document, String, int, int) - Constructor for class com.biomatters.geneious.publicapi.components.GTextArea: See JTextArea.JTextArea(javax.swing.text.Document, String, int, int)
GTextField - Class in com.biomatters.geneious.publicapi.components: Same as JTextField but has undo/redo capability, a popup Edit menu and is linked to the main Edit menu.
GTextField() - Constructor for class com.biomatters.geneious.publicapi.components.GTextField
GTextField(String) - Constructor for class com.biomatters.geneious.publicapi.components.GTextField
GTextField(int) - Constructor for class com.biomatters.geneious.publicapi.components.GTextField
GTextField(String, int) - Constructor for class com.biomatters.geneious.publicapi.components.GTextField
GTextField(Document, String, int) - Constructor for class com.biomatters.geneious.publicapi.components.GTextField
GTextPane - Class in com.biomatters.geneious.publicapi.components: Same as JTextPane but has undo/redo capability, a popup Edit menu and is linked to the main Edit menu.
GTextPane(StyledDocument) - Constructor for class com.biomatters.geneious.publicapi.components.GTextPane: See JTextPane.JTextPane(javax.swing.text.StyledDocument)
GTextPane() - Constructor for class com.biomatters.geneious.publicapi.components.GTextPane: See JTextPane.JTextPane()
GTextPane.MemoryFixedHTMLEditorKit - Class in com.biomatters.geneious.publicapi.components: The HTMLEditorKit used for working around Java bug 6406218.
GTextPane.MemoryFixedHTMLEditorKit() - Constructor for class com.biomatters.geneious.publicapi.components.GTextPane.MemoryFixedHTMLEditorKit
GuiUtilities - Class in com.biomatters.geneious.publicapi.utilities: Provides utility methods for dealing with GUI (swing) components

H

HAIRPIN_FIELD - Static variable in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Displayable field for the hairpin alignment score of the oligo
handleElement(Element) - Method in interface com.biomatters.geneious.publicapi.utilities.xml.FilteredSaxHandler.ElementHandler: Reports a matching element to the callback.
handleElement(Element) - Method in class com.biomatters.geneious.publicapi.utilities.xml.PluginDocumentXmlCollection.ElementHandler: Provides a single child element to the caller of a PluginDocumentXmlCollection.fromXml(org.jdom.Element, com.biomatters.geneious.publicapi.utilities.xml.PluginDocumentXmlCollection.ElementHandler, jebl.util.ProgressListener) call.
handleMessage(Element, String, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerMessageHandler: Handle an incoming or outgoing message
handleSetEnabled(JPanel, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption
handleSetEnabled(JPanel, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption
handleSetEnabled(JLabel, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption
handleSetEnabled(ComponentType, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Set the enabled state of a component.
handleSetEnabled(JPanel, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.RadioOption
handlesTrimAnnotations() - Method in class com.biomatters.geneious.publicapi.plugin.Assembler: Returns true if this assembler handles trim annotations (SequenceAnnotation.TYPE_TRIMMED on input sequences and preserves them on generated contigs.
HAS_ANY_READS_MAPPED_TO_MULTIPLE_LOCATIONS - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: SequenceAlignmentDocuments may have this field to indicate whether or not any reads in it are mapped to multiple locations.
hasAdvancedOptions() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Return true if any option or any child options returns true from Options.Option.isAdvanced()
hasAnyActiveLinks() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
hasAnyPairedReads() - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Query whether there there is at least 1 pair of reads managed by this PairedReadManager.
hasAnyReadsMappedToMultipleLocations() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary
hasBasicOptions() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Return true if any option or any child options returns false from Options.Option.isAdvanced()
hasChromatogramPositionsForResidues() - Method in class com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph
hasChromatogramPositionsForResidues() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
hasChromatogramPositionsForResidues() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph: Tests whether this NucleotideGraph contains information about the position of the base calls, i.e.
hasChromatogramPositionsForResidues() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideGraphSequenceDocument
hasChromatogramPositionsForResidues() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
hasChromatogramPositionsForResidues() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
hasChromatogramValues(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph
hasChromatogramValues(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
hasChromatogramValues(int) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph: Specifies whether it is legal to call NucleotideGraph.getChromatogramValue(int, int) for the specified nucleotide.
hasChromatogramValues(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideGraphSequenceDocument
hasChromatogramValues(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
hasChromatogramValues(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
hasEndGaps() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
hasGraph() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
hashCode() - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogAction
hashCode() - Method in class com.biomatters.geneious.publicapi.databaseservice.QueryField
hashCode() - Method in class com.biomatters.geneious.publicapi.documents.DocumentField
hashCode() - Method in class com.biomatters.geneious.publicapi.documents.DocumentFieldAndValue
hashCode() - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField
hashCode() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument.ReferencedSequence
hashCode() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
hashCode() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup
hashCode() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval
hashCode() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
hashCode() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Calculates a hashCode that is based on this CharSequence's sequence of characters.
hashCode() - Method in class com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument.Taxon
hashCode() - Method in class com.biomatters.geneious.publicapi.documents.URN: Returns the hash code of the string representation of this object.
hashCode() - Method in class com.biomatters.geneious.publicapi.implementations.Percentage
hashCode() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.FolderOrDocuments
hashCode() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature.DocumentSelectionSignatureAtom
hashCode() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentType
hashCode() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
hashCode() - Method in class com.biomatters.geneious.publicapi.plugin.License.PluginLicense
hashCode() - Method in class com.biomatters.geneious.publicapi.plugin.Options.OptionValue
hashCode() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection
hashCode() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
hashCode() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex
hashCode() - Method in class com.biomatters.geneious.publicapi.utilities.Interval
hasInterlacedMates() - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager
hasNext() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Reads
hasProperties() - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument
hasSearchedEntireDatabase() - Method in class com.biomatters.geneious.publicapi.documents.DocumentSearchCache
hasSeqres(String) - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument: Whether the given chain has SEQRES records
hasSequenceQualities() - Method in class com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph
hasSequenceQualities() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
hasSequenceQualities() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
hasSequenceQualities() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph: Tests whether this graph contains information about the confidence in the associated sequence's residues, i.e.
hasSequenceQualities() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideGraphSequenceDocument
hasSequenceQualities() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
hasSequenceQualities() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
hasSetCircular() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: Returns true if SequencePropertiesStorage.setCircular(boolean) has ever been called on this storage properties
hasShutdownOrStartedShuttingDown() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Returns true if this service or its parent service has been GeneiousService.shutdown() or if it is in the process of shutting down.
hasTrims() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
hasValues() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph
HIDDEN_PREFIX - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Qualifiers that have a name that begins with this prefix will be hidden from the user interface
HIDDEN_QUALIFIER_FOR_ACTIVELY_LINKED_PARENTS - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: The name of a qualifier that can be added to annotations on documents which are actively linked to their descendants (see OperationRecordDocument.hasAnyActiveLinks()).
HIDDEN_TYPE_FOR_ACTIVELY_LINKED_PARENTS - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: An annotation type for annotations added to documents which are actively linked to their descendants (see OperationRecordDocument.hasAnyActiveLinks()).
hiddenElementsChanged() - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceListener: Called when one or more hidden elements have been updated, added or removed from a WritableDatabaseService.
hideWarningMessage() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Hides the warning message tooltip for this option if it is visible
HIGH_QUALITY_PERCENT - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The percentage of untrimmed bases in a chromatogram that are high quality.
HinDocument - Class in com.biomatters.geneious.publicapi.implementations.structure: A Hin molecular structure document.
HinDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.structure.HinDocument
humanJoin(Iterable) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Like join(", ", values), except that the last value is separated with " and " instead of ", ".
humanReadableName - Variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: Human readable name of document type.
hyperlinkUpdate(HyperlinkEvent) - Method in class com.biomatters.geneious.publicapi.components.DefaultHyperlinkListener

I

ICON - Static variable in class com.biomatters.geneious.publicapi.plugin.GeneiousAction

Icons - Class in com.biomatters.geneious.publicapi.plugin

Stores a set of different sized versions of the same icon.

Icons(Icon) - Constructor for class com.biomatters.geneious.publicapi.plugin.Icons

Creates Icons from a single sized Icon.

Icons(Icon, Icon) - Constructor for class com.biomatters.geneious.publicapi.plugin.Icons

Creates Icons from two sized Icons.

iconsChanged() - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousServiceListener

Called when service icons (GeneiousService.getIcons()) changed.

IconUtilities - Class in com.biomatters.geneious.publicapi.utilities

Utilities for loading and manipulating images and icons.

immutableCopyOf(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities

Constructs an immutable CharSequence that consists of the same sequence of characters as the specified CharSequence.

ImmutableSequence - Class in com.biomatters.geneious.publicapi.documents.sequence

An implementation of a SequenceDocument that is immutable and has very low memory usage.

ImmutableSequence.Builder - Class in com.biomatters.geneious.publicapi.documents.sequence

Provides a system for building a list of ImmutableSequence which are even more compact than normal by analyzing patterns in the names of sequences.

ImmutableSequence.Builder() - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence.Builder

immutableSequenceFromXML(Element) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence

Recreates this sequence from XML returned from a previous call to ImmutableSequence.toXML(boolean).

ImmutableSequenceImplementation - Class in com.biomatters.geneious.publicapi.documents.sequence

Despite this class being public, it is only public for implementation reasons.

ImmutableSequenceImplementation() - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation

importDocuments(File, DocumentFileImporter.ImportCallback, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter

Import document(s) from file into a callback

importDocuments(Options, File, DocumentFileImporter.ImportCallback, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter

Import document(s) from file into a callback.

importDocuments(File, DocumentFileImporter.ImportCallback, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridImporter

This method is for internal use by Geneious.

importDocuments(File, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities

Imports documents from a file into an in memory list.

importDocuments(File, DocumentFileImporter, ImportUtilities.ActionWhenInvalid, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.ImportUtilities

Imports the given file with a specific importer and default options.

importDocuments(File, DocumentFileImporter.ImportCallback, ImportUtilities.ActionWhenInvalid, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.ImportUtilities

Equivalent to importDocuments(file, callback, actionWhenInvalid, ImportDocumentType.AskUser, progressListener)

importDocuments(File, DocumentFileImporter.ImportCallback, ImportUtilities.ActionWhenInvalid, ImportUtilities.ImportDocumentType, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.ImportUtilities

Imports the given file, using any available importer.

importDocuments(File, DocumentFileImporter.ImportCallback, ImportUtilities.ActionWhenInvalid, ImportUtilities.ImportDocumentType, SequenceDocument.Alphabet, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.ImportUtilities

Imports the given file, using any available importer.

importDocumentsFromMultipleFiles(List<File>, DocumentFileImporter.ImportCallback, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter

Deprecated.

use DocumentFileImporter.importDocumentsFromMultipleFilesReturningUnimported(Options, java.util.List, com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.ImportCallback, jebl.util.ProgressListener) instead

importDocumentsFromMultipleFilesReturningUnimported(Options, List<File>, DocumentFileImporter.ImportCallback, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter

An alternative to

DocumentFileImporter.importDocuments(java.io.File, com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.ImportCallback, jebl.util.ProgressListener)

that importers which import multiple files may implement.

importDocumentsToDatabase(File, WritableDatabaseService, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities

Imports documents from a file into a database.

importFastaAlignment(File, SequenceDocument.Alphabet, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.ImportUtilities

Imports the given fasta file as a list of aligned sequences, padding the sequences with trailing gaps if necessary.

importFastaSequences(File, SequenceDocument.Alphabet, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.ImportUtilities

Imports the given fasta file as a list of unaligned sequences.

ImportUtilities - Class in com.biomatters.geneious.publicapi.utilities

Provides methods for importing documents into Geneious.

ImportUtilities.ActionWhenInvalid - Enum in com.biomatters.geneious.publicapi.utilities

Specifies what to do when a sequence with invalid bases/residues is encountered during import

ImportUtilities.ImportDocumentType - Enum in com.biomatters.geneious.publicapi.utilities

whether to import ambiguous files as alignments of sequence lists.

incrementOrderingRevisionNumber() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument

Increments the value returned from DefaultSequenceListDocument.getOrderingRevisionNumber() to indicate that alignments that reference sequences by index in this list should discard their reference.

INDEL_DISAGREEMENTS - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField

The number of alignment columns with a disagreement between two or more sequences and at least one is a gap

All small SequenceAlignmentDocuments have this field.

indexOf(CharSequence) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence

Get the index of the first character of the first occurrence of the specified sub sequence in this sequence

indexOf(CharSequence, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence

Get the index of the first character of the first occurrence of the specified sub sequence in this sequence, starting at the specified index

initialize(GeneiousServiceListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService

initialize(File, File) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin

An initialization method which plugins should override to obtain the plugin's installation directory and a user writable directory.

initialize(GeneiousServiceListener) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService

Constructor method - initializes the service.

initialize() - Static method in class com.biomatters.geneious.publicapi.plugin.TestGeneious

Initialize various public api utility methods.

initializeAllBundledPlugins() - Static method in class com.biomatters.geneious.publicapi.plugin.TestGeneious

Initializes all plugins that are bundled with Geneious so that that various PluginUtilities methods are able to access them.

initializeAllPlugins() - Static method in class com.biomatters.geneious.publicapi.plugin.TestGeneious

Initializes all available plugins so that that various PluginUtilities methods are able to access them.

initializePlugins(String...) - Static method in class com.biomatters.geneious.publicapi.plugin.TestGeneious

Initializes plugins so that various PluginUtilities methods are able to access them.

initializePlugins(GeneiousPlugin...) - Static method in class com.biomatters.geneious.publicapi.plugin.TestGeneious

Initializes plugins so that various PluginUtilities methods are able to access them.

initializeService(GeneiousServiceListener) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService

Initializes this service by setting up internal handlers and delegating to GeneiousService.initialize(GeneiousServiceListener).

initializeWorkAroundJavaBug6406218() - Static method in class com.biomatters.geneious.publicapi.components.GTextPane

Initializes a work-around for Java bug 6406218 so that any usages of GTextPane, GEditorPane, JTextPane and #JEditorPane don't result in memory leaks.

InputStreamFromRandomAccessFile - Class in com.biomatters.geneious.publicapi.utilities

Provides an InputStream view into the current position in a RandomAccessFile.

InputStreamFromRandomAccessFile(RandomAccessFile) - Constructor for class com.biomatters.geneious.publicapi.utilities.InputStreamFromRandomAccessFile

Constructs a new input stream from the current location in the given random access file

insert(int, CharSequence) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence

insert(int, CharSequence) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation

insert(int, CharSequence) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence

Creates a copy of this SequenceCharSequence with the specified CharSequence inserted at the specified index.

insertGaps(int, int, int[], int[]) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence

Creates a new sequence identical to this one except with some gaps inserted.

insertGaps(int, int, int[], int[]) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation

insertItemAt(Object, int) - Method in class com.biomatters.geneious.publicapi.components.GComboBox

integerArrayFromXML(Element) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage

Converts some xml created from a preious call to SequencePropertiesStorage.integerArrayToXML(String, int[]) back to an integer array.

integerArrayToXML(String, int[]) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage

Converts an integer array to xml, storing them in a compact way if possible.

integerArrayToXML(Geneious.MajorVersion, String, int[]) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage

Converts an integer array to xml, storing them in a compact way if possible.

Intern<T> - Class in com.biomatters.geneious.publicapi.utilities

Manages manually interning Objects (like String.intern()) except this implemenation avoids the following pitfalls with String.intern() Objects are not interned into the permgen (the permgen is independent of the normal heap and limited to 64MB by default), so using String.intern too often can result in OutOfMemory errors when you have plently of free space This implemenation is faster than String.intern since it doesn't have to deal with garbage collecting weak references Disadvantages of this implemenation include

Intern() - Constructor for class com.biomatters.geneious.publicapi.utilities.Intern

intern(T) - Method in class com.biomatters.geneious.publicapi.utilities.Intern

Interns an object.

intersects(Interval) - Method in class com.biomatters.geneious.publicapi.utilities.Interval

intersectsWith(SequenceAnnotationInterval) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval

Determines if this interval intersects with another interval.

intersectsWith(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval

Equivalent to calling intersectsWith(new SequenceAnnotationInterval(minimumIndexOfOtherInterval, maximumIndexOfOtherIntervalInclusive))

intersectsWithInCircularSequence(SequenceAnnotationInterval, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval

Determines if this interval intersects with another interval in a circular sequence.

intersectsWithInCircularSequence(int, int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval

Equivalent to calling

intersectsWithInCircularSequence(new SequenceAnnotationInterval(minimumIndexOfOtherInterval, maximumIndexOfOtherIntervalInclusive),circularSequenceLength)

Interval - Class in com.biomatters.geneious.publicapi.utilities

Represents a directional interval.

Interval(int, int) - Constructor for class com.biomatters.geneious.publicapi.utilities.Interval

Interval(Element) - Constructor for class com.biomatters.geneious.publicapi.utilities.Interval

Reconstructs this interval from a previously serialized element

Interval(int) - Constructor for class com.biomatters.geneious.publicapi.utilities.Interval

Constructs a length 1 interval consisting of a single value.

Interval(String) - Constructor for class com.biomatters.geneious.publicapi.utilities.Interval

Constructs an interval from its String representation.

IntList - Class in com.biomatters.geneious.publicapi.utilities

Similar to a java.util.List but uses primitive ints instead of Integers for better performance.

IntList() - Constructor for class com.biomatters.geneious.publicapi.utilities.IntList

IntList.Array - Class in com.biomatters.geneious.publicapi.utilities

An implementation of an IntList that is mutable and backed by an array

IntList.Array(int) - Constructor for class com.biomatters.geneious.publicapi.utilities.IntList.Array

Construct a new empty IntList with the given intial capacity

intValue() - Method in class com.biomatters.geneious.publicapi.implementations.EValue

intValue() - Method in class com.biomatters.geneious.publicapi.implementations.Percentage

INVISIBLE_ANNOTATION_TYPE_PREFIX - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation

Annotations whose type (SequenceAnnotation.getType()) has this prefix are not visible in the sequence viewer.

invokeAndWait(Runnable) - Static method in class com.biomatters.geneious.publicapi.utilities.ThreadUtilities

Equivalent to SwingUtilities.invokeAndWait(Runnable) except it correctly handles spurious wake ups which can cause the method to return before the runnable has completed.

invokeLater(Runnable) - Static method in class com.biomatters.geneious.publicapi.utilities.ThreadUtilities

Delegates to EventQueue.invokeLater(Runnable).

invokeNowOrLater(Runnable) - Static method in class com.biomatters.geneious.publicapi.utilities.ThreadUtilities

If the current thread is the swing thread, then immediately calls the given parameter's run method otherwise, this function is a wrapper to EventQueue.invokeLater(Runnable).

invokeNowOrWait(Runnable) - Static method in class com.biomatters.geneious.publicapi.utilities.ThreadUtilities

If the current thread is the swing thread, then this method immediately calls the given parameter's run method otherwise, this method is a wrapper to EventQueue.invokeAndWait(Runnable).

invokeNowOrWait(Callable<T>) - Static method in class com.biomatters.geneious.publicapi.utilities.ThreadUtilities

Invokes the given Callable in the swing thread and returns the result.

invokeWhileHoldingLock(Runnable) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk

Invokes a runnable while holding the synchronization lock for this sequence list on disk.

is64BitOS() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities

Return true if we are running under any 64-bit operating system.

is64BitVM() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities

Returns true if this Java VM is probably 64 bit (rather than 32 bit).

IS_FREE_END_GAPS - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField

Whether this alignment has free end gaps.

isAboveOrBelowAnotherViewer() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer.ViewerLocation

Whether or not the viewer is above/below another viewer in a split layout.

isAdjacent(Interval) - Method in class com.biomatters.geneious.publicapi.utilities.Interval

isAdvanced() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option

determine whether or not this option is advanced (appears in the advanced options panel)

isAlignment(PluginDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentType

isAlignment(AnnotatedPluginDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentType

isAlignmentAndNotSequence(PluginDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentType

isAlignmentAndNotSequence(AnnotatedPluginDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentType

isAlignmentOrContig() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor

isAllGaps() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence

Returns true if this seqeuence consists entirely of gap ('-') characters.

isAllGaps(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities

Returns true if the given sequence is either empty or contains only gaps.

isAllInMemory() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ExternalSort

Returns true if all this data is in memory (i.e.

isAllowSequencesInNucleotideAlignments() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature

get whether a signature created forNucleotideSequences() or forNucleotideAndProteinSequences() allows sequences in alignments as well as from stand-alone sequences

isAllowSequencesInProteinAlignments() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature

get whether a signature created using forProteinSequences() or forNucleotideAndProteinSequences() allows sequences in alignments as well as from stand-alone sequences

isAminoAcidSequence(PluginDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentType

isAminoAcidSequence(AnnotatedPluginDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentType

isAnimated() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph

isAnyReferenceSequenceFromAnUndissolvedContig() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties

isAtMinimumZoom() - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel

isAvailableMemoryLessThan(long) - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities

Checks whether the available memory has dropped below the specified amount.

isAvailableToWorkflows() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions

isBesideAnotherViewer() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer.ViewerLocation

Whether or not the viewer is beside another in a split layout.

isBestSerializedToXmlRatherThanBinaryFormat() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument

Returns true if this sequence would be best serialized using DefaultSequenceDocument.toXML() rather than DefaultSequenceDocument.writeObject(java.io.DataOutput, jebl.util.ProgressListener).

isBetweenBases() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval

Returns true if this interval represents a position between 2 bases, which is represented by the special case where SequenceAnnotationInterval.getMaximumIndex()==SequenceAnnotationInterval.getMinimumIndex()-1.

isBorderOpaque() - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel.RoundedLineBorder

isBothStrandsCovered() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Coverage

isBrowsable() - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService

A Database Service is browsable if its documents are viewed when it is selected in the service tree.

isBrowse() - Method in interface com.biomatters.geneious.publicapi.databaseservice.Query

Returns true if this is a browse query, false otherwise.

isCanceled() - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame

isCanceled() - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback

Returns true if this retrieval has been canceled.

isCanceled() - Method in exception com.biomatters.geneious.publicapi.plugin.DocumentOperationException

Returns true if the document operation exception was thrown because the operation was canceled, usually in response to ProgressListener.isCanceled returning true.

isCaseSensitive() - Method in class com.biomatters.geneious.publicapi.plugin.Findable.FindOptions

Should the search be case sensitive?

isCenterText() - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption

Returns true if the label text will be drawn centered

isCharSequenceKnownToBeImmutable(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities

Returns true if we know that the specified charSequence will never change.

isCircular() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation

isCircular() - Method in interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument

Returns true if this sequence is circular.

isCircular() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument

isCircular() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument

Is this a circular sequence?

isCircular() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage

isCircularSequence(int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever

Returns true if this sequence is circular

isClient() - Static method in class com.biomatters.geneious.publicapi.plugin.Geneious

isCommercialUser() - Static method in class com.biomatters.geneious.publicapi.plugin.License

Checks if the currently active license is for a commercial user of the software.

isContig() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument

Returns false by default.

isContig() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument

isContig() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument

isDedicatedExtensionViewer() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor

isDefaultVisible() - Method in class com.biomatters.geneious.publicapi.documents.DocumentField

Returns true if this field is visible in the document table by default.

isDefaultVisibleInTable() - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType

Are the fields of this note type visible in the document table by default.

isDeleted() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService

Get whether this database folder is deleted.

isDeletedFromWritableDatabaseService() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument

Returns true if this document was originally in a WritableDatabaseService but has now been deleted.

isDirectedLeft() - Method in enum com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval.Direction

isDirectedLeft() - Method in class com.biomatters.geneious.publicapi.utilities.Interval

isDirectedRight() - Method in enum com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval.Direction

isDisplayableInSecondaryFrame() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory

If false then this viewer will never be available in secondary frames which the user opens (by double clicking or selecting and "Open in new window" action).

isDisplayedInHelpPanel() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory

A viewer can be displayed as a tab in the help panel on the right hand side of the main window.

isDocumentGenerator() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation

Does this DocumentOperation generate documents? (i.e.

isDocumentGenerator() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper

isEditable() - Method in class com.biomatters.geneious.publicapi.databaseservice.ComboboxSearchOption

isEditable() - Method in class com.biomatters.geneious.publicapi.documents.DocumentField

Returns true if the user is able to edit the value of this field.

There is a subtle distinction between this and #isNeverEditable(), which determines if a field was generated automatically and hence is never editable.

isEditable() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument

true if this alignment is editable.

isEditable() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument

isEditable() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument

isEditingAnnotationType(String) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation

isEmpty() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult

isEmpty() - Method in class com.biomatters.geneious.publicapi.utilities.IntList.Array

isEmpty() - Method in class com.biomatters.geneious.publicapi.utilities.IntList

Returns true if this list is empty IntList.size()==0)

isEmulatingTerminal() - Method in class com.biomatters.geneious.publicapi.utilities.Execution

Return true if this process is being executed by emulating a terminal.

isEnabled() - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogAction

Returns the enabled state of the DialogAction.

isEnabled() - Method in interface com.biomatters.geneious.publicapi.components.GComboBox.EnabledStateProvider

Provide the enabled state of this item.

isEnabled() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction

isEnabled() - Method in class com.biomatters.geneious.publicapi.plugin.Options

Determine if these options appear enabled.

isEnabled() - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions

Determine if these MultipleOptions appear enabled.

isEnabled() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option

Query whether this option is currently enabled.

isEnabled() - Method in class com.biomatters.geneious.publicapi.plugin.Options.OptionValue

Determine whether this option value is enabled not.

isEnabled() - Method in interface com.biomatters.geneious.publicapi.utilities.CallSoon.EnabledProvider

isEndGap(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence

Returns true if the given endex is an end gap (i.e.

isEndGap(int, int) - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsHelper

Is this residue an end gap? End gaps are gaps at either end of the sequence.

isEnumeratedField() - Method in class com.biomatters.geneious.publicapi.documents.DocumentField

Returns true if this field is enumerated, that is it can only have a value from a predifined set of values.

isEnumeratedField() - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField

An enumerated field can only take a value from a predifined set of values (of String type).

isFileNameAllowed(String) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities

Will check a filename for validity on all platforms supported by Geneious.

isFillHorizontalSpace() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option

Should this option's component fill all available horizontal space.

isFindAll() - Method in class com.biomatters.geneious.publicapi.plugin.Findable.FindOptions

Returns true if this search should find all occurrences rather than just a single occurrence.

isFinishedAddingOutputDocuments() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument

isForwards() - Method in class com.biomatters.geneious.publicapi.plugin.Findable.FindOptions

Get search direction.

isFreeEndGapAlignment() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument

True if this alignment was built using free end gaps.

isFreeEndGapAlignment() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument

isFreeEndGapAlignment() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument

isFreeEndGapAlignment() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever

isFromStart() - Method in class com.biomatters.geneious.publicapi.plugin.Findable.FindOptions

Get search start location.

isGap(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence

Returns true if the given endex is a gap.

isGap(int) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation

Return true if the character at the specified gapped sequence index is an internal gap or end gap Characters beyond the ends of the gapped sequence are assumed to be non-gaps (for consistency with SequenceGapInformation.getUngappedIndexOfThisOrPreviousResidue(int)) therefore isGap(x) where x<0 or x>=gappedSequenceLength will return false.

isGenerateContigs() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput

Returns whether or not contigs should be produced by the assembly.

isHeadless() - Static method in class com.biomatters.geneious.publicapi.plugin.Geneious

isHidden() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier

Returns true if this qualifier is hidden from the user interface.

isHorizontallyCompact() - Method in class com.biomatters.geneious.publicapi.plugin.Options

Returns true if these options or any ancestor options have been set as horizontally compact using Options.setHorizontallyCompact(boolean).

isImmutableSequenceHeader(byte) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation

isInLocalRepository() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument

Returns true if this document is in the user's persistent storage repository (a WritableDatabaseService - either a local or shared database) or false if it is an in memory only document.

isInMainToolbar() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction

isInMainToolbar() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions

isInPopupMenu() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction

isInPopupMenu() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions

isInterestedInParentDescendants() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback

isInterestedInParentDescendants() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback.Wrapper

isInterlacedWithAllReadsHavingSameExpectedDistance() - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager

isInternalGap(int) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation

Return true if the character at the specified gapped sequence index is an internal (non-end) gap.

isInvisibleAnnotationType(String) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation

Returns true if annotations of this type are not visible to the user.

isJava6OrLater() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities

Deprecated.

As of version 6.0.0 Geneious is Java 6 or later only, this will always return true

isJava7OrLater() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities

Returns true if this VM is Java 7 or later.

isLargeIcons() - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar

isLinkPairedReadsInRow(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout

Returns true if pairs reads in the given row number are linked (i.e.

isLinux() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities

Return true if we are running under any Linux operating system.

isLocal() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService

Is this a local database rather than a shared Database.

isLocal() - Method in class com.biomatters.geneious.publicapi.documents.URN

isMac() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities

Return true if we are running under any Mac operating system.

isModal() - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions

Get whether the dialog should be modal.

isMoreGeneral(DocumentSelectionSignature[], DocumentSelectionSignature[]) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature

Returns true if all possible documents accepted by potentiallyMoreSpecificSignatures will also be accepted by potentiallyMoreGeneralSignatures.

isMoreOptions() - Method in class com.biomatters.geneious.publicapi.components.MoreOptionsButton

Whether this button is in the "More Options" or "Fewer Options" state.

isNetworkConnectionError() - Method in exception com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceException

When true, exception caused by a failure to connect to an external database.

isNeverEditable() - Method in class com.biomatters.geneious.publicapi.documents.DocumentField

returns true if the field should never be editable, because it is one of the standard fields for which the value is auto-generated.

isNucleotideSequence(PluginDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentType

isNucleotideSequence(AnnotatedPluginDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentType

isNucleotideSequenceSignature() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature

get whether this signature was created using forNucleotideSequences() or forNucleotideAndProteinSequences()

isPairwise() - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation.InputProperties

isPluginLicenseActive(GeneiousPlugin, License.PluginLicense, boolean) - Static method in class com.biomatters.geneious.publicapi.plugin.License

Check if a trial or purchased license is active for the given plugin license.

isPredominantlyRna(CharSequence, int) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities

Checks whether a sequence is predominantly RNA (rather than DNA).

isProOnly() - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation

isProOnly() - Method in class com.biomatters.geneious.publicapi.plugin.Assembler

If true, this assembler will be always disabled when the user doesn't have an active license.

isProOnly() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileExporter

Deprecated.

Importers and exporters should not be restricted, all though this method still functions.

isProOnly() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter

Deprecated.

Importers and exporters should not be restricted, all though this method still functions.

isProOnly() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory

Returns true if DocumentViewers created by this factory requires an active license.

isProOnly() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction

isProOnly() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions

If true, this action will be always disabled when the user doesn't have an active license.

isProOnly() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousPreference

Deprecated.

Does this preference requires an active license?

isProOnly() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService

This function returns true if the service requires an active license.

isProOnly() - Method in class com.biomatters.geneious.publicapi.plugin.Options

Determine whether or not these options require an active license.

isProOnly() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option

determine whether or not this option requires an active license.

isProOnly() - Method in class com.biomatters.geneious.publicapi.plugin.Options.OptionValue

determine whether or not this option requires an active license.

isProOnly() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph

Does this graph require an active license? The default implementation returns false.

isProteinSequenceSignature() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature

get whether this signature was created using forProteinSequences() or forNucleotideAndProteinSequences()

isProVersion() - Static method in class com.biomatters.geneious.publicapi.plugin.License

Checks whether Geneious currently has an active license, eg.

isQueryCentricAlignment() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument

Returns true if this alignment is a query centric alignment.

isQueryCentricAlignment() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument

isReadOnly() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService

Returns whether or not this folder is read only.

isReadOnly() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument

isReadOnlyAnnotationType(String) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation

isReferencedDocumentReversed(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument

Sequence direction.

isReferencedDocumentReversed(int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument

isReferencedDocumentReversed(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument

isReferenceSequnece(int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever

Get whether or not the specified sequence is a reference sequence in an alignment or contig.

isRefine(Options) - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation

isRemoteRun(Options) - Static method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation

Returns true if the job represented by the given options (from DocumentOperation.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[])) is a remote run.

isRestoreDefaultApplies() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option

Returns true if calling Options.restoreDefaults() should restore this setting to its default value

isRestoreDefaultApplies() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionGrabOption

isRestorePreferenceApplies() - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption

isRestorePreferenceApplies() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option

Returns true if calling Options.restorePreferences() should restore this setting to its value saved in preferences, and Options.Option.shouldSaveValue() returns true

isRestorePreferenceApplies() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionGrabOption

isRetinaDisplay() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities

isReversed() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence

Determine if this sequence is reversed (i.e.

isReversed() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation

isReversedSequence(SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities

Determines if a SequenceDocument is reversed or not based on whether its name ends with SequenceExtractionUtilities.REVERSED_NAME_SUFFIX or not.

isReversedSequence(int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever

Get the direction of the specified sequence.

isRna(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities

Checks whether a sequence is RNA (rather than DNA) based on whether the sequence contains either a T/t or a U/u first.

isRunningApplication() - Static method in class com.biomatters.geneious.publicapi.plugin.TestGeneious

Deprecated.

Use Geneious.isClient() instead

isRunningFromScript() - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities

isRunningTest() - Static method in class com.biomatters.geneious.publicapi.plugin.TestGeneious

Checks whether we are currently running from tests or whether Geneious is running normally.

isSafeToKillOutReadThread() - Method in class com.biomatters.geneious.publicapi.utilities.Execution

Tells Execution whether it is safe to end the thread which reads stdout from the process.

isSaveUnusedReads() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput

Returns whether or not unused reads should be saved by the assembly.

isSaveUsedReads() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput

Returns whether or not used reads should be saved by the assembly.

isSaveUsedReadsIncludeMates() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput

Returns whether or not the mates of used reads (even if that mate doesn't map) should be saved by the assembly.

isSelectable() - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption

isSelected() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction.ToggleAction

Whether or not this action is selected

isSelected() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.SequenceAnnotationWrapper

isSequence(PluginDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentType

isSequence(AnnotatedPluginDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentType

isSequenceList(PluginDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentType

isSequenceList(AnnotatedPluginDocument) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentType

isServer() - Static method in class com.biomatters.geneious.publicapi.plugin.Geneious

isSetReferencedDocumentsOnContig() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput

Returns true if the assembly implementation should set referenced documents/sequences (see SequenceAlignmentDocument.getReferencedSequence(int)) for the reads on generated contigs.

isSetUp() - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService

If this method returns false then the user will not be allowed to choose this service as a search target until they have set it up.

isShowLabels() - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar

isSimilarAnnotation(SequenceAnnotation, SequenceAnnotation) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator

Determines whether an annotation generated by this generator is similar enough to an existing annotation on a sequence such that the generated annotation should not be displayed to the user.

isSingleAlignment() - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation.InputProperties

isSingleContigMappingToReferenceSequenceFromSeparateDocument() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties

isSingleInputContig() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties

returns true if there is just a single contig being provided as input to the assembler.

isSolaris() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities

Deprecated.

Geneious is no longer supported on Solaris

isSolarisSparc() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities

Deprecated.

Geneious is no longer supported on Solaris

isSolarisX86() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities

Deprecated.

Geneious is no longer supported on Solaris

isSpanningComponent() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option

Does the default generated panel treat this options's component as spanning when it has an empty label? Spanning means that it uses the entire width of the panel rather than just the space to the right of all the labels.

isStandardImplementation() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument

Returns true if this sequence implementation is either DefaultNucleotideSequence or DefaultAminoAcidSequence or DefaultNucleotideGraphSequence.

isStateAssignableFrom(State, State) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities

Same as stateA.getCanonicalStates().containsAll(stateB.getCanonicalStates()) except that for NucleotideStates and AminoAcidStates it caches the result.

isStoredInConnectedNonLocalDatbase() - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType

If a note type is stored in a non-local database then the user should be notified when editing it because they may effect other users.

issueWarning(String, String) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback

Initiate a message to user from retriever.

isTrimmed(int, int) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever

Get whether or not the specified position in the specified sequence is trimmed or not

isTruncatedAtMaximumIndex() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval

Checks whether the interval is incomplete and really finishes after the maximum index.

isTruncatedAtMinimumIndex() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval

Checks whether the interval is incomplete and really beings before the minimum index.

isUnread() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument

Returns true if document retrieved by agent and not yet seen by user.

isUserModificationAllowed() - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField

If false then the user should not be allowed to modify or remove this note field through any user interface.

isValueHtml() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier

Scans through the string to check if there appears to be valid angle brackets in it (an equal number, in the right order).

isVisible() - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Panel

isVisible() - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType

isVisible() - Method in class com.biomatters.geneious.publicapi.plugin.Options

Return true if the graphical component that displays these options would be visible to the user when the panel is showing.

isVisible() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option

Get the visibility of the graphical component for this option.

isVisibleOnlyWhenEnabled() - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption

Returns true if the component for this option will only be visible if the option is enabled.

isWindows() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities

Return true if we are running under any Windows operating system.

iterator() - Method in class com.biomatters.geneious.publicapi.utilities.Interval

iterator() - Method in class com.biomatters.geneious.publicapi.utilities.WeakReferenceList

Gets an iterator over all objects added to this class that are still strongly referenced.

J

join(String, Iterable) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Concatenates values (calling toString() on each of them), interleaved with the separator string.
JournalArticleDocument - Interface in com.biomatters.geneious.publicapi.documents.types: Interface for plugin documents containing a Journal Article.
JournalArticleDocument.Utils - Class in com.biomatters.geneious.publicapi.documents.types
JournalArticleDocument.Utils() - Constructor for class com.biomatters.geneious.publicapi.documents.types.JournalArticleDocument.Utils

K

KEY_ALIGNMENT_OPTIONS - Static variable in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
KEY_ALIGNMENT_SCORE - Static variable in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
KEY_ANNOTATION_GROUP - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Name of a qualifier whose value identifies a group that this annotation belongs to on a single sequence.
KEY_CREATED_BY - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: A special key used to identify the origin of this annotation.
KEY_DOCUMENT_SIZE - Static variable in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
KEY_MATCH_REGIONS - Static variable in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
KEY_MODIFIED_BY - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: A special key to identify the last modifier of this annotation.
KEY_NEXUS_TREE_DISTANCE_MATRIX - Static variable in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
KEY_SEARCH_SUBFOLDERS - Static variable in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: All WritableDatabaseServices return a CheckboxSearchOption with this code from getExtendedSearchOptions()
KEY_SEARCH_TYPE - Static variable in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: All WritableDatabaseServices return a TextOrSimilaritySearchOption with this code from getExtendedSearchOptions(false)
KEY_SEQUENCE_RESIDUES - Static variable in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument

L

LEFT - Static variable in class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption
length() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ByteBackedCharSequence
License - Class in com.biomatters.geneious.publicapi.plugin: Provides access to the current Geneious user license state, the names of various versions of Geneious, and support for being notified when the license key status changes.
License.PluginLicense - Class in com.biomatters.geneious.publicapi.plugin: Represents the properties of a license which is used to activate a "pay-for" plugin or feature.
License.PluginLicense(String, String, int, int) - Constructor for class com.biomatters.geneious.publicapi.plugin.License.PluginLicense
linkDocumentsInDatabase(ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument: Links the documents in this record together.
listFromXML(Element, Class<? extends T>) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Deserializes a list of XMLSerializable elements which were serialized using XMLSerializer.listToXML(String, java.util.List).
listToString(List<String>) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Converts a list of Strings into a single String which can be converted back to a list via StringUtilities.stringToList(String)
listToXML(String, List<? extends XMLSerializable>) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Serializes a list of XMLSerializable elements which can be deserialized using XMLSerializer.listFromXML(org.jdom.Element, Class).
loadDocumentsBeforeRunningOperation() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: Returns true if this operation requires that the caller load the PluginDocuments of all input AnnotatedPluginDocuments and the PluginDocuments of all referenced AnnotatedPluginDocuments into memory before invoking performOperation.
loadDocumentsBeforeRunningOperation() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
loadDocumentsBeforeShowingOptions() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: Returns true if this operation requires that the caller load the PluginDocuments of all input AnnotatedPluginDocuments and the PluginDocuments of all referenced AnnotatedPluginDocuments into memory before invoking getOptions.
loadDocumentsBeforeShowingOptions() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
loadInternalPluginDocuments() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory
LOCAL_DATABASE_SERVICE_UNIQUE_ID - Static variable in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: The unique ID of the local database root "Local" service.
locateSummaryDocument(AnnotatedPluginDocument, AnnotatedPluginDocument[]) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: Locate summary document of fully downloaded documents.
locationChanged(GeneiousService) - Method in class com.biomatters.geneious.publicapi.plugin.OperationLocationOptions.LocationChangedListener: Used to indicate that the value returned from OperationLocationOptions.getSelectedLocation() has changed.
longValue() - Method in class com.biomatters.geneious.publicapi.implementations.EValue
longValue() - Method in class com.biomatters.geneious.publicapi.implementations.Percentage
LOW_QUALITY_PERCENT - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The percentage of untrimmed bases in a chromatogram that are low quality.

M

MalformedURNException - Exception in com.biomatters.geneious.publicapi.documents: Exception indicating an incorrectly formatted URN.
MalformedURNException(String) - Constructor for exception com.biomatters.geneious.publicapi.documents.MalformedURNException: Default constructor.
matches(List<? extends AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: Check whether this selection signature matches these documents.
matches(DocumentSelectionSignature[], List<? extends AnnotatedPluginDocument>) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature
matches(DocumentSelectionSignature[], Class[]) - Static method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature: Deprecated.
Use DocumentSelectionSignature.matches(DocumentSelectionSignature[], java.util.List) instead.
max(Geneious.MajorVersion...) - Static method in enum com.biomatters.geneious.publicapi.plugin.Geneious.MajorVersion
MAXIMUM_HTML_LENGTH - Static variable in interface com.biomatters.geneious.publicapi.documents.PluginDocument: PluginDocument.toHTML() should not return a string greater in length to this.
MAXIMUM_HTML_TEXT_LENGTH - Static variable in class com.biomatters.geneious.publicapi.implementations.structure.DefaultMolecularStructureDocument: the maximum length of the DefaultMolecularStructureDocument.getStructure() text returned from DefaultMolecularStructureDocument.toHTML()
MAXIMUM_SEQUENCE_LENGTH - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: SequenceListDocuments may have this field which indicates the maximum length of all the sequences in the document.
mayDiscardInformation() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileExporter: Return true if exporter does not preserve the complete geneious document, i.e if an export and a subsequent import may result in a loss of some data items (say annotations, notes etc).
MEDIMUM_QUALITY_PERCENT - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The percentage of untrimmed bases in a chromatogram that are medium quality.
MENU_MASK - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: The key modifier for the Ctrl key on all operating systems except Mac OS, on which it is the Command key.
merge(List<SequenceAnnotationInterval>) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Deprecated.
equivalent to calling merge(intervals, true)
merge(List<SequenceAnnotationInterval>, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Merges a list of intervals, i.e.
merge(List<Interval>) - Static method in class com.biomatters.geneious.publicapi.utilities.Interval: Merges a list of intervals, i.e.
META_KEY_STRING - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: System-dependent string used to represent the META key
milliTime() - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities: Returns a counter that can be used for measuring elapsed time in milliseconds.
min(Geneious.MajorVersion...) - Static method in enum com.biomatters.geneious.publicapi.plugin.Geneious.MajorVersion
MINIMUM_SEQUENCE_LENGTH - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: SequenceListDocuments may have this field which indicates the minimum length of all the sequences in the document.
MODIFIED_DATE_FIELD - Static variable in interface com.biomatters.geneious.publicapi.documents.PluginDocument: A field indicating when a document was last modified.
MolDocument - Class in com.biomatters.geneious.publicapi.implementations.structure: A Mol molecular structure document.
MolDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.structure.MolDocument
MOLECULAR_STRUCTURE_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: MolecularStructureDocument document type
MolecularStructureDocument - Interface in com.biomatters.geneious.publicapi.documents.types: Interface representing 3D model data of a molecular structure.
MOLECULE_TYPE_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Visible, editable field representing the molecule type of a sequence (eg, mRNA or AA) Use this field in all documents which should have a displayable molecule type value.
MoreOptionsButton - Class in com.biomatters.geneious.publicapi.components: A button which toggles between "More Options" and "Fewer Options" with a down and up arrow icon respectively (the text can be changed).
MoreOptionsButton(boolean) - Constructor for class com.biomatters.geneious.publicapi.components.MoreOptionsButton: Construct a MoreOptionsButton with the specified initial more/fewer state.
MoreOptionsButton(boolean, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.MoreOptionsButton: Construct a MoreOptionsButton with the specified initial more/fewer state and specify whether it should change state automatically when clicked.
MoreOptionsButton(boolean, boolean, Action) - Constructor for class com.biomatters.geneious.publicapi.components.MoreOptionsButton: Construct a MoreOptionsButton with the specified initial more/fewer state, specify whether it should change state automatically when clicked and provide an action for the button.
mouseClicked(MouseEvent) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: The mouse has been clicked in this sequence graph.
mouseDragged(MouseEvent) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: The mouse has been dragged in this sequence graph (with a drag starting inside the graph, not outside it).
mouseEntered(MouseEvent) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: The mouse has left this sequence graph.
mouseExited(MouseEvent) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: The mouse has left this sequence graph.
mouseMoved(MouseEvent) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: The mouse has been moved in this sequence graph.
mousePressed(MouseEvent) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: The mouse has been pressed in this sequence graph.
mouseReleased(MouseEvent) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: The mouse has been released in this sequence graph.
moveDocument(AnnotatedPluginDocument, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Move a document that currently reside elsewhere in this database to this folder.
moveTo(WritableDatabaseService) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Move this entire database folder to a new location.
moveToOptions(Options, String, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Moves this Option from its current parent Options to another parent Options.
moveToOptions(Options, String, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.RadioOption
MultiThreadedProcessingSystem<T> - Class in com.biomatters.geneious.publicapi.utilities: A utility class providing a system in which a number of elements are each independently processed in some way (in multiple threads) before calling finishedProcessing on each element in the same order as they originally came in.
MultiThreadedProcessingSystem(String, int, int, int) - Constructor for class com.biomatters.geneious.publicapi.utilities.MultiThreadedProcessingSystem
MultiThreadedTask<ResultType> - Class in com.biomatters.geneious.publicapi.utilities: Manages a task that can be split over multiple threads.

Example 1: to split a task across multiple threads (1 per processor), use:
MultiThreadedTask() - Constructor for class com.biomatters.geneious.publicapi.utilities.MultiThreadedTask: Creates a task split over a number of threads equal to the number of processors available on this machine.
MultiThreadedTask(int) - Constructor for class com.biomatters.geneious.publicapi.utilities.MultiThreadedTask: Creates a task split over the specified number of threads

N

name - Variable in enum com.biomatters.geneious.publicapi.documents.Condition: Human readable name of condition.
NAME - Static variable in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
NAME_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Visible, editable field representing a document's name All documents have this field.
nameChanged() - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousServiceListener: Called when service name (GeneiousService.getName()) has changed.
namespace - Variable in class com.biomatters.geneious.publicapi.documents.URN: The name of the organization which defines the rules on name allocation for this URN.
NCBI_CODON_START - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Qualifier name used by NCBI for the frame of a CDS (may be 1, 2 or 3).
NCBI_TRANSL_TABLE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Qualifier name used by NCBI for the translation table number of a CDS
newFileInputStreamWithRetry(File) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Attempts to create a new FileInputStream, but if it fails, retries a few times until it succeeds.
newFileOutputStreamWithRetry(File) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Attempts to create a new FileOutputStream, but if it fails with a FileNotFoundException, retries a few times until it succeeds.
newRandomAccessFileWithRetry(File, String) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Attempts to create a new RandomAccessFile, but if it fails, retries a few times until it succeeds.
NICE_NAME - Static variable in interface com.biomatters.geneious.publicapi.documents.sequence.AminoAcidSequenceDocument: A nice named to describe the documents represented by this class.
NICE_NAME - Static variable in interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument: A nice name to describe the documents represented by this class.
NO - Static variable in class com.biomatters.geneious.publicapi.components.Dialogs: An action with "No" as its label.
NO_END_GAPS - Static variable in class com.biomatters.geneious.publicapi.implementations.EndGapsHelper: A EndGaps instance that always returns false from EndGapsHelper.isEndGap(int, int)
noLongerViewed(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.NoLongerViewedListener: The user is no longer interested in viewing this.
NoLongerViewedListener - Class in com.biomatters.geneious.publicapi.plugin: May be supplied by a DocumentViewer (via getNoLongerViewedListener) to be notified when they are no longer being viewed.
NoLongerViewedListener() - Constructor for class com.biomatters.geneious.publicapi.plugin.NoLongerViewedListener
NOTES - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Free text entered by the user
notifyListenersSearchCancelled() - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: Notifies all listeners registered via addSearchCancelledListener().
NUCLEOTIDE_SEQUENCE_COUNT - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The number of nucleotide sequences in an alignment or set of sequences.
NUCLEOTIDE_SEQUENCE_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: NucleotideSequenceDocument document type
NUCLEOTIDE_SEQUENCES_WITH_MATES_COUNT - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The number of nucleotide sequences in an alignment or set of sequences that have mates (i.e.
NUCLEOTIDE_SEQUENCES_WITH_QUALITY_COUNT - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The number of nucleotide sequences in an alignment or set of sequences that have quality data (i.e.
NUCLEOTIDE_SIMILARITY_SEARCH_TYPE - Static variable in class com.biomatters.geneious.publicapi.databaseservice.TextOrSimilaritySearchOption
NucleotideGraph - Interface in com.biomatters.geneious.publicapi.documents.sequence: Optional phred-like quality information on the residues of a sequence, and an optional chromatogram graph.
NucleotideGraph.ImmutableGraphProvider - Interface in com.biomatters.geneious.publicapi.documents.sequence: An interface a NucleotideGraph may implement to indicate it can provide an immutable instance of itself.
NucleotideGraphSequenceDocument - Interface in com.biomatters.geneious.publicapi.documents.sequence: A nucleotide sequence with an underlying "graph".
NUCLEOTIDES_COUNT - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: SequenceListDocuments may have this field which indicates the total number of nucleotides in all sequences in the document
NucleotideSequenceDocument - Interface in com.biomatters.geneious.publicapi.documents.sequence: An interface for a nucleotide sequence.
NUMBER_OF_MAPPED_LOCATIONS - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: SequenceDocuments may have this field to indicate the number of places the read maps to the reference sequence(s).
NUMBER_OF_STOP_CODONS - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The minimum number of stop codons for this sequence (for a single frame, across all frames)
numberOfArgs() - Method in enum com.biomatters.geneious.publicapi.documents.Condition: Returns the number of values associated with this condition.
NwoDocument - Class in com.biomatters.geneious.publicapi.implementations.structure: A Nwo molecular structure document.
NwoDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.structure.NwoDocument

O

objectChanged() - Method in class com.biomatters.geneious.publicapi.utilities.WeakSimpleListenerManager
offsetBy(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Returns a new interval offset to the right by the given distance from this interval
offsetBy(int) - Method in class com.biomatters.geneious.publicapi.utilities.Interval: Creates a new interval, offset from this interval by the specified amount
OK - Static variable in class com.biomatters.geneious.publicapi.components.Dialogs: An action with "OK" as its label.
OK_CANCEL - Static variable in class com.biomatters.geneious.publicapi.components.Dialogs: Use this to specify that a dialog should have "OK" and "Cancel" buttons.
OK_ONLY - Static variable in class com.biomatters.geneious.publicapi.components.Dialogs: Use this to specify that a dialog should have just an "OK" button.
OLIGO_DOC_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: Primer/Oligo sequence document type
OLIGO_TYPE_FIELD - Static variable in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Displayable field for the type of oligo (see OligoSequenceDocument.OligoType) The value of this field is the toString() value of the OligoType object
OligoSequenceDocument - Class in com.biomatters.geneious.publicapi.implementations.sequence: A sequence document which represents an olgionucleotide such as a Primer or DNA probe.
OligoSequenceDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: PluginDocument requirement, do not call directly
OligoSequenceDocument(String, String, CharSequence, Date) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Create an OligoSequenceDocument "from scratch".
OligoSequenceDocument(NucleotideSequenceDocument) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Create an OligoSequenceDocument from an existing SequenceDocument.
OligoSequenceDocument.OligoType - Enum in com.biomatters.geneious.publicapi.implementations.sequence: The possible types of oligos
openDocumentsInNewWindow(List<AnnotatedPluginDocument>) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Opens a new Geneious window and displays these documents in all available document viewers that match these documents.
openUrl(URL) - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities: Open the system's default browser and navigate to the specified url.
openUrl(URL, Component) - Static method in class com.biomatters.geneious.publicapi.utilities.SystemUtilities: Open the system's default browser and navigate to the specified url.
operand - Variable in class com.biomatters.geneious.publicapi.documents.Constraint
OperationLocationOptions - Class in com.biomatters.geneious.publicapi.plugin: An Options that provides the ability to pick between running an Operation on the local computer or on a supported GeneiousService.
OperationLocationOptions.LocationChangedListener - Class in com.biomatters.geneious.publicapi.plugin: Used to indicate that the value returned from OperationLocationOptions.getSelectedLocation() has changed.
OperationLocationOptions.LocationChangedListener() - Constructor for class com.biomatters.geneious.publicapi.plugin.OperationLocationOptions.LocationChangedListener
OperationRecordDocument - Class in com.biomatters.geneious.publicapi.documents: Stores references to the input and output documents a from single DocumentOperation.
OperationRecordDocument() - Constructor for class com.biomatters.geneious.publicapi.documents.OperationRecordDocument: PluginDocument deserialization constructor.
OperationRecordDocument(List<URN>, String, long) - Constructor for class com.biomatters.geneious.publicapi.documents.OperationRecordDocument: Creates an operation record whose documents added later using OperationRecordDocument.addOutputDocument(URN) will be inactively linked (see OperationRecordDocument.hasAnyActiveLinks())
OperationRecordDocument(List<URN>, List<URN>, String, long, Element) - Constructor for class com.biomatters.geneious.publicapi.documents.OperationRecordDocument: Creates an operation record whose documents added later using OperationRecordDocument.addOutputDocument(URN) will be actively linked (see OperationRecordDocument.hasAnyActiveLinks())
Options - Class in com.biomatters.geneious.publicapi.plugin: Provides options used by DocumentOperations, SequenceAnnotationGenerators and SequenceGraphs.
Options() - Constructor for class com.biomatters.geneious.publicapi.plugin.Options: For use by subclasses only; Equivalent to Options(getClass()) .
Options(Class) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options: Construct a new options.
Options(Class, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options: Construct a new options.
Options(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options: Constructor for XML Serialization.
Options.Alignment - Enum in com.biomatters.geneious.publicapi.plugin: Used the specifying how other options for a Options.RadioOption are layed out.
Options.BooleanOption - Class in com.biomatters.geneious.publicapi.plugin: An option that stores a Boolean and is represented graphically as a check box.
Options.BooleanOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.BooleanOption: Constructor for XML Serialization.
Options.BooleanOption(String, String, Boolean) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.BooleanOption: Construct a new Boolean option
Options.ButtonOption - Class in com.biomatters.geneious.publicapi.plugin: Provides the user with a button which may have actions associated with it by calling Options.ButtonOption.addActionListener(java.awt.event.ActionListener).
Options.ButtonOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption: Constructor for XML Serialization.
Options.ButtonOption(String, String, String, Icon, int) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption: Construct a new ButtonOption.
Options.ButtonOption(String, String, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption: Construct a new ButtonOption with no icon, and center aligned.
Options.ComboBoxOption<ValueType extends Options.OptionValue> - Class in com.biomatters.geneious.publicapi.plugin: An option that provides the user with a list of options in a combo box
Options.ComboBoxOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption: Constructor for XML Serialization.
Options.ComboBoxOption(String, String, ValueType[], ValueType) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption: Construct a new ComboBoxOption.
Options.ComboBoxOption(String, String, List<? extends ValueType>, ValueType) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption: Construct a new ComboBoxOption.
Options.ComponentCreator - Interface in com.biomatters.geneious.publicapi.plugin: An interface for creating components on demand for use with Options.addCustomComponent(com.biomatters.geneious.publicapi.plugin.Options.ComponentCreator)
Options.DateOption - Class in com.biomatters.geneious.publicapi.plugin: An option that stores a date.
Options.DoubleOption - Class in com.biomatters.geneious.publicapi.plugin: An option that stores an Double and is displayed graphically to the user as a single line text field with a spinner (up and down arrow) on the right-hand side
Options.DoubleOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.DoubleOption: Constructor for XML Serialization.
Options.DoubleOption(String, String, Double) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.DoubleOption: Construct a new Double option
Options.DoubleOption(String, String, Double, Double, Double) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.DoubleOption: Construct a new Double option
Options.EditableComboBoxOption - Class in com.biomatters.geneious.publicapi.plugin: Like a ComboBoxOption, but besides letting the user choose one of the preconfigured default values, also allows arbitrary custom strings to be entered.
Options.ExecutableFileSelectionOption - Class in com.biomatters.geneious.publicapi.plugin: Provides the user with an executable file name and provides assistance with finding the location of it.
Options.ExecutableFileSelectionOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ExecutableFileSelectionOption: Constructor for XML Serialization.
Options.ExecutableFileSelectionOption(String, String, String, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ExecutableFileSelectionOption: Construct a new ExecutableFileOption.
Options.FileSelectionOption - Class in com.biomatters.geneious.publicapi.plugin: Provides functionality to let the user choose a file.
Options.FileSelectionOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption: Constructor for XML Serialization.
Options.FileSelectionOption(String, String, String, String[], String, FilenameFilter) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption: Construct a new FileSelectionOption.
Options.IntegerOption - Class in com.biomatters.geneious.publicapi.plugin: An option that stores an Integer and is displayed graphically to the user as a single line text field with a spinner (up and down arrow) on the right-hand side.
Options.IntegerOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.IntegerOption: Constructor for XML Serialization.
Options.IntegerOption(String, String, Integer, int, int) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.IntegerOption: Construct a new Integer option
Options.IntegerOption(String, String, Integer) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.IntegerOption: Construct a new Integer option
Options.LabelOption - Class in com.biomatters.geneious.publicapi.plugin: An option that is only used for display purposes.
Options.LabelOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.LabelOption
Options.LabelOption(String, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.LabelOption: Constructs a LabelOption.
Options.MultipleLineStringOption - Class in com.biomatters.geneious.publicapi.plugin: An option that stores a String and is displayed to the user as a multiple line text area
Options.MultipleLineStringOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.MultipleLineStringOption: Constructor for XML Serialization.
Options.MultipleLineStringOption(String, String, String, int, boolean) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.MultipleLineStringOption: Construct a new MultipleLineStringOption
Options.MultipleOptions - Class in com.biomatters.geneious.publicapi.plugin: Stores the multiple options added using Options.addMultipleOptions(String, Options, boolean) and provides methods to access the current values (Options.MultipleOptions.getValues()) and to add change listeners (Options.MultipleOptions.addChangeListener(org.virion.jam.util.SimpleListener) and to change the enabled state Options.MultipleOptions.setEnabled(boolean).
Options.Option<ValueType,ComponentType extends JComponent> - Class in com.biomatters.geneious.publicapi.plugin: The base class of all types of options.
Options.Option(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.Option: Constructor for XML Serialization.
Options.Option(String, String, ValueType) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.Option: Construct a new option
Options.OptionValue - Class in com.biomatters.geneious.publicapi.plugin: Possible values that a Options.RadioOption or Options.ComboBoxOption can take on.
Options.OptionValue(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.OptionValue
Options.OptionValue(String, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.OptionValue: Construct a new option value.
Options.OptionValue(String, String, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.OptionValue: Construct a new option value.
Options.OptionValue(String, String, String, boolean) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.OptionValue: Construct a new option value.
Options.OptionValue(String, String, String, boolean, Icons) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.OptionValue: Construct a new option value.
Options.PageChooserType - Enum in com.biomatters.geneious.publicapi.plugin: An enum listing the different types of child options choosers.
Options.RadioOption<ValueType extends Options.OptionValue> - Class in com.biomatters.geneious.publicapi.plugin: An option that provides the user with a list of radio buttons to select one of
Options.RadioOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.RadioOption: Constructor for XML Serialization.
Options.RadioOption(String, String, ValueType[], ValueType, Options.Alignment) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.RadioOption: Construct a new Radio option.
Options.RadioOption.DependentPosition - Enum in com.biomatters.geneious.publicapi.plugin
Options.StringOption - Class in com.biomatters.geneious.publicapi.plugin: An option that stores a String and is displayed graphically to the user as a single line text field.
Options.StringOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.StringOption: Constructor for XML Serialization.
Options.StringOption(String, String, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.StringOption
Options.StringOption(String, String, String, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.StringOption: Construct a new String option
OptionsPanel - Class in com.biomatters.geneious.publicapi.components: A panel that lays out label/component pairs vertically.
OptionsPanel() - Constructor for class com.biomatters.geneious.publicapi.components.OptionsPanel: Calls OptionsPanel(true, true).
OptionsPanel(boolean, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.OptionsPanel
OptionsPanel.RoundedLineBorder - Class in com.biomatters.geneious.publicapi.components: The border used for boxes when OptionsPanel.beginBorderedGroup(String, boolean).
OptionsPanel.RoundedLineBorder(String, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.OptionsPanel.RoundedLineBorder: Constructs a new SimpleLineBorder.
ORGANISM_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Visible, editable field representing a document's organism Use this field in all documents which should have a displayable organism value.
OutputStreamThatCountsBytesWritten - Class in com.biomatters.geneious.publicapi.utilities: An OutputStream that counts the number of bytes written to it and forwards write methods on to another output stream.
OutputStreamThatCountsBytesWritten(OutputStream) - Constructor for class com.biomatters.geneious.publicapi.utilities.OutputStreamThatCountsBytesWritten: Construct a new OutputStreamThatCountsBytesWritten that counts the number of bytes written to it and forwards write calls on to another stream.
OutputStreamToRandomAccessFile - Class in com.biomatters.geneious.publicapi.utilities: Provides an OutputStream view into the current position in a RandomAccessFile.
OutputStreamToRandomAccessFile(RandomAccessFile) - Constructor for class com.biomatters.geneious.publicapi.utilities.OutputStreamToRandomAccessFile: Constructs a new output stream from the current location in the given random access file
OverlayIcons - Class in com.biomatters.geneious.publicapi.components: An Icons wrapper that overlays one or more sets of Icons on top of a base set of Icons.
OverlayIcons(Icons, Icons...) - Constructor for class com.biomatters.geneious.publicapi.components.OverlayIcons: Create a new Icons that overlays one or more Icons on top of a base Icons.
OVERRIDE_DOCUMENT_TYPE_KEY - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: A PluginDocument may return a value from PluginDocument.getFieldValue(String) with this fieldCodeName to change the class used to get the document type of the document.
overrideClass - Variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: an alternative class that can be set on a document using DocumentType.OVERRIDE_DOCUMENT_TYPE_KEY to change its icon etc.

P

pack() - Method in class com.biomatters.geneious.publicapi.components.GDialog
paint(Graphics) - Method in class com.biomatters.geneious.publicapi.components.GTextPane
paintBorder(Component, Graphics, int, int, int, int) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel.RoundedLineBorder
PairedReadManager - Class in com.biomatters.geneious.publicapi.implementations: Keeps track of which sequences in a list of sequences are paired together and their paired distances.
PairedReadManager(int) - Constructor for class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Constructs a new paired read manager with this many sequences, none of which are initially paired.
PairedReadManager(Element) - Constructor for class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Reconstructs a PairedReadManager previously serialized to XML using PairedReadManager.toXml(String).
PairedReadManager(GeneiousObjectInputStream) - Constructor for class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Reconstructs a PairedReadManager previously serialized using PairedReadManager.toOutputStream(com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectOutputStream).
PairedReadManager.Builder - Class in com.biomatters.geneious.publicapi.implementations: Allows for the construction of a PairedReadManager where the data resides on disk instead of in memory.
PairedReadManager.Builder() - Constructor for class com.biomatters.geneious.publicapi.implementations.PairedReadManager.Builder: Creates a new PairedReadManager.Builder
PairedReadManager.Orientation - Enum in com.biomatters.geneious.publicapi.implementations: Represents the relative orientation for a set of interlaced reads.
PairedReads - Interface in com.biomatters.geneious.publicapi.documents.sequence: Provides data about whether nucleotide sequences are paired together and their expected paired distance.
parseElement(String) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Parses some XML.
parseElementPreserveText(String) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Parses some XML text which was generated using StringUtilities.formatElementPreserveText(org.jdom.Element).
PartiallyWritableDatabaseService - Class in com.biomatters.geneious.publicapi.databaseservice: A database service which allows partial editing of its contents (either the deleting or renaming or editing field values of some or all of its contents).
PartiallyWritableDatabaseService() - Constructor for class com.biomatters.geneious.publicapi.databaseservice.PartiallyWritableDatabaseService
PdbDocument - Class in com.biomatters.geneious.publicapi.implementations.structure: A PDB molecular structure document.
PdbDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument
PdbDocument(String, Date, String) - Constructor for class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument: Construct a PDB document from contents in PDB format.
PdbDocument(String, Date, String, URN) - Constructor for class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument: Construct an externally retrieved PDB document.
PERCENT_GC_FIELD - Static variable in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Displayable field for GC percent of the oligo
Percentage - Class in com.biomatters.geneious.publicapi.implementations: Just like a double, but the toString() method displays it as a percentage with the specified number of decimal places.
Percentage(double, int) - Constructor for class com.biomatters.geneious.publicapi.implementations.Percentage
Percentage() - Constructor for class com.biomatters.geneious.publicapi.implementations.Percentage: this constructor is only here to be used immediately prior to fromXML.
Percentage(double) - Constructor for class com.biomatters.geneious.publicapi.implementations.Percentage
performBackgroundCalculations(ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Perform some background calculations in a non AWT thread before this graph is drawn.
performed(GDialog) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogAction: Called when button clicked, before dialog is disposed.
performOperation(AnnotatedPluginDocument[], ProgressListener, Options) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: Create document(s) from a set of documents.
performOperation(AnnotatedPluginDocument[], ProgressListener, Options, SequenceSelection, DocumentOperation.OperationCallback) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: Do not use.
performOperation(AnnotatedPluginDocument[], ProgressListener, Options, SequenceSelection) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: A convenience method to call DocumentOperation.performOperation(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], jebl.util.ProgressListener, Options, SequenceSelection, com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback) .
performOperation(List<AnnotatedPluginDocument>, ProgressListener, Options) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: A convenience method for calling DocumentOperation.performOperation(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], jebl.util.ProgressListener, Options)
performOperation(ProgressListener, Options, AnnotatedPluginDocument...) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation: A convenience method for calling DocumentOperation.performOperation(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], jebl.util.ProgressListener, Options)
performOperation(AnnotatedPluginDocument[], ProgressListener, Options) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
performOperation(AnnotatedPluginDocument[], ProgressListener, Options, SequenceSelection, DocumentOperation.OperationCallback) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
performOperation(AnnotatedPluginDocument[], ProgressListener, Options, SequenceSelection) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.Wrapper
performOperation(AnnotatedPluginDocument[], ProgressListener, Options, SequenceSelection, DocumentOperation.OperationCallback) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation
PhylogenyDocument - Class in com.biomatters.geneious.publicapi.documents.types: A document containing an alignment and one or more trees whose tips are the sequences (i.e.
PhylogenyDocument() - Constructor for class com.biomatters.geneious.publicapi.documents.types.PhylogenyDocument
PhylogenyDocument(SequenceAlignmentDocument) - Constructor for class com.biomatters.geneious.publicapi.documents.types.PhylogenyDocument
PluginDocument - Interface in com.biomatters.geneious.publicapi.documents: PluginDocument defines the interface for a Document created by a plugin.
PluginDocument.ReferencedDocumentsAlwaysLoaded - Interface in com.biomatters.geneious.publicapi.documents: PluginDocuments can optionally implement this empty interface to signify that they generally require their referenced documents when they are deserialized and for general use such as viewing the document, even if those referenced documents have not been modified since this PluginDocument was last saved.
PluginDocument.ReferencedDocumentsNotLoaded - Interface in com.biomatters.geneious.publicapi.documents: PluginDocuments can optionally implement this empty interface to signify that they don't require their referenced documents when they are deserialized and for general use such as viewing the document.
PluginDocument.SizeRequiredToLoadIntoMemoryProvider - Interface in com.biomatters.geneious.publicapi.documents: A PluginDocument may implement this interface to indicate to Geneious the amount of memory it will probably require in order to load the document.
pluginDocumentFileDataFromXml(Element, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Deserializes the name of a file serialized using DocumentUtilities.pluginDocumentFileDataToXml(org.jdom.Element, java.io.File, boolean) checking for corruption such as the file disappearing, changing in size or reducing to 0 bytes in size.
pluginDocumentFileDataToXml(Element, File, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Provides a system for storing a reference to an arbitrary immutable file from within a PluginDocument.
pluginDocumentToXml(PluginDocument, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Converts a PluginDocument to XML, handling the case where the PluginDocument may or may not implement XMLSerializableWithProgress.
pluginDocumentToXml(Geneious.MajorVersion, PluginDocument, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Converts a PluginDocument to XML, handling the case where the PluginDocument may or may not implement XMLSerializableWithProgress.
PluginDocumentXmlCollection - Class in com.biomatters.geneious.publicapi.utilities.xml: Provides a system for serializing and deserializing a PluginDocument that contains a large number of sub-elements so that all the elements do not need to be in memory simultaneously.
PluginDocumentXmlCollection() - Constructor for class com.biomatters.geneious.publicapi.utilities.xml.PluginDocumentXmlCollection
PluginDocumentXmlCollection.ElementHandler - Class in com.biomatters.geneious.publicapi.utilities.xml
PluginDocumentXmlCollection.ElementHandler() - Constructor for class com.biomatters.geneious.publicapi.utilities.xml.PluginDocumentXmlCollection.ElementHandler
PluginPreferences<T extends Options> - Class in com.biomatters.geneious.publicapi.plugin: Allows a plugin to provide Options based preferences that are displayed in the Geneious Preferences dialog.
PluginPreferences() - Constructor for class com.biomatters.geneious.publicapi.plugin.PluginPreferences
PluginUtilities - Class in com.biomatters.geneious.publicapi.plugin: Provides various functionality to access other installed plug-ins.
PluginUtilities.WritableDatabaseServicesListener - Class in com.biomatters.geneious.publicapi.plugin: A listener used for notifying when root WritableDatabaseServices are added or removed in Geneious.
PluginUtilities.WritableDatabaseServicesListener() - Constructor for class com.biomatters.geneious.publicapi.plugin.PluginUtilities.WritableDatabaseServicesListener
POSITION_AMINO_ACID_TRANSLATION_FREQUENCIES - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that amino acid translation frequencies returns from SequenceViewerExtension.StatisticsSection.getVerticalPosition()
POSITION_CODON_FREQUENCIES - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that codon frequencies returns from SequenceViewerExtension.StatisticsSection.getVerticalPosition()
POSITION_COVERAGE - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that the read length distributions returns from SequenceViewerExtension.StatisticsSection.getVerticalPosition()
POSITION_EXPECTED_ERRORS - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that the expected errors returns from SequenceViewerExtension.StatisticsSection.getVerticalPosition()
POSITION_FREQUENCIES - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that the frequencies of nucleotides or amino acids in the sequence returns from SequenceViewerExtension.StatisticsSection.getVerticalPosition()
POSITION_IDENTICAL_SITES - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that the number of identical sites returns from SequenceViewerExtension.StatisticsSection.getVerticalPosition()
POSITION_MEAN_CONFIDENCE - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that the mean confidence returns from SequenceViewerExtension.StatisticsSection.getVerticalPosition()
POSITION_NUMBER_OF_SEQUENCES - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that the number of sequences returns from SequenceViewerExtension.StatisticsSection.getVerticalPosition()
POSITION_PERCENTAGE_PAIRWISE_IDENTITY - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that the percentage pairwise identity returns from SequenceViewerExtension.StatisticsSection.getVerticalPosition()
POSITION_PROTEIN_EXTINCTION_COEFFICIENT - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that the protein molecular weight returns from SequenceViewerExtension.StatisticsSection.getVerticalPosition()
POSITION_PROTEIN_ISOELECTRIC_POINT - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that the protein molecular weight returns from SequenceViewerExtension.StatisticsSection.getVerticalPosition()
POSITION_PROTEIN_MOLECULAR_WEIGHT - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that the protein molecular weight returns from SequenceViewerExtension.StatisticsSection.getVerticalPosition()
POSITION_QUALITY_THRESHOLD_COUNTS - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that the quality threshold counts (e.g.
POSITION_READ_LENGTHS - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that the read length distributions returns from SequenceViewerExtension.StatisticsSection.getVerticalPosition()
POSITION_SEQUENCE_LENGTH - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: The value that the sequence length returns from SequenceViewerExtension.StatisticsSection.getVerticalPosition()
POST_TRIM_LENGTH - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The length of a chromatogram after trimming.
premiumVersionName() - Static method in class com.biomatters.geneious.publicapi.plugin.License: Deprecated.
there never was and there will never be a premium version of Geneious. Deprecated in API 4.600 (Geneious 6.0.0)
premiumVersionPrefix() - Static method in class com.biomatters.geneious.publicapi.plugin.License: Deprecated.
there never was and there will never be a premium version of Geneious. Deprecated in API 4.600 (Geneious 6.0.0)
preserveSequenceOrder(Options) - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation
PRIMER - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup: A group of annotations created when designing primers, including SequenceAnnotation.TYPE_PRIMER_BIND, SequenceAnnotation.TYPE_PRIMER_BIND_REVERSE.
PRIMER_DIMER_FIELD - Static variable in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Displayable field for the primer-dimer alignment score of the oligo
PRIMER_INFO_NOTE_CODE - Static variable in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Code for the "Primer Info" note type.
print(Graphics2D, Dimension, int, Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable: print a single page of this component.
print(Graphics2D, Dimension, int, Options) - Method in class com.biomatters.geneious.publicapi.plugin.ExtendedPrintable.Wrapper
println(String, Object...) - Static method in class com.biomatters.geneious.publicapi.utilities.GeneralUtilities: Prints a line to standard out, with a leading message displaying the time and a trailing message indicating the location in the source code of the calling method.
process(T) - Method in class com.biomatters.geneious.publicapi.utilities.MultiThreadedProcessingSystem: Processes a single entry previously added using MultiThreadedProcessingSystem.add(Object)
ProgressFrame - Class in com.biomatters.geneious.publicapi.components: An implementation of ProgressListener which displays progress using a progress bar and a cancel button in a Frame.
ProgressFrame(String, String) - Constructor for class com.biomatters.geneious.publicapi.components.ProgressFrame: Creates a progress frame manager to display the progress of a potentially time-consuming operation.
ProgressFrame(String, String, Window) - Constructor for class com.biomatters.geneious.publicapi.components.ProgressFrame: Creates a progress frame manager to display the progress of a potentially time-consuming operation.
ProgressFrame(String, String, long, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.ProgressFrame: Deprecated.
use ProgressFrame.ProgressFrame(String, String) instead
ProgressFrame(String, String, long, boolean, Window) - Constructor for class com.biomatters.geneious.publicapi.components.ProgressFrame: Deprecated.
use ProgressFrame.ProgressFrame(String, String, java.awt.Window) instead
ProgressInputStream - Class in com.biomatters.geneious.publicapi.utilities: An InputStream that reports progress to a ProgressListener and queries the ProgressListener about when to cancel, throwing an ProgressInterruptedIOException when it should cancel.
ProgressInputStream(ProgressListener, InputStream, long) - Constructor for class com.biomatters.geneious.publicapi.utilities.ProgressInputStream: Constructs an object to monitor the progress of an input stream.
ProgressInputStream(ProgressListener, File) - Constructor for class com.biomatters.geneious.publicapi.utilities.ProgressInputStream: Constructs an object to monitor the progress of an input stream reading from a file.
ProgressInputStream.ProgressInterruptedIOException - Exception in com.biomatters.geneious.publicapi.utilities: An InterruptedIOException that was thrown by a ProgressInputStream because its ProgressListener signaled that the operation was aborted.
ProgressInputStream.ProgressInterruptedIOException() - Constructor for exception com.biomatters.geneious.publicapi.utilities.ProgressInputStream.ProgressInterruptedIOException
ProgressInputStream.ProgressInterruptedIOException(String) - Constructor for exception com.biomatters.geneious.publicapi.utilities.ProgressInputStream.ProgressInterruptedIOException
proOnlyButtonName(String) - Static method in class com.biomatters.geneious.publicapi.plugin.License: Useful for renaming a feature when there is no license active.
ProOnlyComponents - Class in com.biomatters.geneious.publicapi.components: A set of components which automatically become disabled if the user does not have an active license.
ProOnlyComponents.Button - Class in com.biomatters.geneious.publicapi.components: Same as a GButton but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.Button(GeneiousAction) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Button
ProOnlyComponents.CheckBox - Class in com.biomatters.geneious.publicapi.components: Same as a JCheckBox but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.CheckBox(String) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBox
ProOnlyComponents.CheckBox(String, ProOnlyComponents.CheckBox.ProOnlySuffix) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBox
ProOnlyComponents.CheckBox.ProOnlySuffix - Enum in com.biomatters.geneious.publicapi.components
ProOnlyComponents.CheckBoxMenuItem - Class in com.biomatters.geneious.publicapi.components: Same as a JCheckBoxMenuItem but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.CheckBoxMenuItem(GeneiousAction) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBoxMenuItem
ProOnlyComponents.ComboBox - Class in com.biomatters.geneious.publicapi.components: Same as a GComboBox but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.ComboBox(ComboBoxModel) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ComboBox
ProOnlyComponents.ComboBox(Object[]) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ComboBox
ProOnlyComponents.ComboBox(Vector<?>) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ComboBox
ProOnlyComponents.ComboBox() - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ComboBox
ProOnlyComponents.ComboBox(boolean) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ComboBox
ProOnlyComponents.Label - Class in com.biomatters.geneious.publicapi.components: Same as a JLabel but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.Label(String) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Label
ProOnlyComponents.Label(String, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Label
ProOnlyComponents.Menu - Class in com.biomatters.geneious.publicapi.components: Same as a JMenu but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.Menu(String) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Menu
ProOnlyComponents.MenuItem - Class in com.biomatters.geneious.publicapi.components: Same as a JMenuItem but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.MenuItem(GeneiousAction) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.MenuItem
ProOnlyComponents.Panel - Class in com.biomatters.geneious.publicapi.components: A Panel that wraps a component that is only available if the user has an active license.
ProOnlyComponents.Panel(JComponent, String) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Panel: Creates a Panel that wraps a component that is only available if the user has an active license.
ProOnlyComponents.ToggleButton - Class in com.biomatters.geneious.publicapi.components: Same as a JToggleButton but automatically becomes disabled if the user does not have an active license.
ProOnlyComponents.ToggleButton(GeneiousAction.ToggleAction) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ToggleButton
proOnlyName(String) - Static method in class com.biomatters.geneious.publicapi.plugin.License: Useful for renaming a feature when there is no license active.
PROTEIN_SEQUENCE_COUNT - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The number of amino acid sequences in an alignment or set of sequences.
PROTEIN_SEQUENCE_LIST_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: Protein Sequence List document type
PROTEIN_SIMILARITY_SEARCH_TYPE - Static variable in class com.biomatters.geneious.publicapi.databaseservice.TextOrSimilaritySearchOption
proVersionName() - Static method in class com.biomatters.geneious.publicapi.plugin.License: Deprecated.
there is no "Pro" version anymore, Geneious is Geneious. Consider using Geneious.getName() instead. Deprecated in API 4.600 (Geneious 6.0.0)
proVersionSuffix() - Static method in class com.biomatters.geneious.publicapi.plugin.License: Deprecated.
there is no "Pro" version anymore, Geneious is Geneious. Consider using License.restrictedName(boolean) instead. Deprecated in API 4.600 (Geneious 6.0.0)
providesUnusedReads() - Method in class com.biomatters.geneious.publicapi.plugin.Assembler: Returns true if this assembler can inform the Assembler.Callback about all reads that couldn't be assembled.
providesUsedReads() - Method in class com.biomatters.geneious.publicapi.plugin.Assembler: Returns true if this assembler can inform the Assembler.Callback about all reads that could be assembled.
providesUsedReadsIncludeMates() - Method in class com.biomatters.geneious.publicapi.plugin.Assembler: Returns true if this assembler can inform the Assembler.Callback about the mates of all reads that could be assembled.
PUBLICATION_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: PublicationDocument document type
PublicationDocument - Interface in com.biomatters.geneious.publicapi.documents.types: Interface for plugin documents containing a publication.
PublicationDocument.Utils - Class in com.biomatters.geneious.publicapi.documents.types
PublicationDocument.Utils() - Constructor for class com.biomatters.geneious.publicapi.documents.types.PublicationDocument.Utils

Q

Query - Interface in com.biomatters.geneious.publicapi.databaseservice: An interface that produces a common ancestor for various queries.
Query.Factory - Class in com.biomatters.geneious.publicapi.databaseservice: Provides methods for creating queries.
Query.Factory() - Constructor for class com.biomatters.geneious.publicapi.databaseservice.Query.Factory
QueryField - Class in com.biomatters.geneious.publicapi.databaseservice: Basic block for building advanced search queries.
QueryField(DocumentField, Condition[]) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.QueryField: Constructor.
QueryField() - Constructor for class com.biomatters.geneious.publicapi.databaseservice.QueryField: Empty constructor used only during XML serialisation.

R

read(GeneiousObjectInputStream) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.ExternalSort.Serializer: reads an element from a stream
read() - Method in class com.biomatters.geneious.publicapi.utilities.InputStreamFromRandomAccessFile
read(byte[]) - Method in class com.biomatters.geneious.publicapi.utilities.InputStreamFromRandomAccessFile
read(byte[], int, int) - Method in class com.biomatters.geneious.publicapi.utilities.InputStreamFromRandomAccessFile
read() - Method in class com.biomatters.geneious.publicapi.utilities.ProgressInputStream: Overrides FilterInputStream.read to update the progress monitor after the read.
read(byte[]) - Method in class com.biomatters.geneious.publicapi.utilities.ProgressInputStream: Overrides FilterInputStream.read to update the progress listener after the read.
read(byte[], int, int) - Method in class com.biomatters.geneious.publicapi.utilities.ProgressInputStream: Overrides FilterInputStream.read to update the progress listener after the read.
readBooleans(DataInputStream, boolean[], int) - Static method in class com.biomatters.geneious.publicapi.utilities.DataInputOutputUtilities: Reads some boolean values to a stream, using 1 bit per value (rather than 1 byte per value if you use DataOutputStream.writeBoolean(boolean)
readByte() - Method in class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectInputStream
readByteArray() - Method in class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectInputStream: Reads an array from this stream that was written using GeneiousObjectOutputStream.writeByteArray(byte[]).
readInt() - Method in class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectInputStream
readIntArray() - Method in class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectInputStream: Reads an array from this stream that was written using GeneiousObjectOutputStream.writeIntArray(int[]).
readObject(GeneiousObjectInputStream) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Reads a graph previously written using DefaultNucleotideGraph.writeObject(GeneiousObjectOutputStream , NucleotideGraph)
readObject(DataInput) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Reads a graph previously written using DefaultNucleotideGraph.writeObject(java.io.DataOutput, NucleotideGraph)
readObject(GeneiousObjectInputStream) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Reads a instance of an ImmutableSequence that was previously written using SequenceCharSequence.writeObject(GeneiousObjectOutputStream, jebl.util.ProgressListener)
readObject(DataInput, byte) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
readObject(GeneiousObjectInputStream) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Reads data previously created using SequenceAnnotation.writeObject(GeneiousObjectOutputStream) It is a good idea to use a GeneiousObjectInputStream when deserializing lots of annotations.
readObject(DataInput) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Reads data previously created using SequenceAnnotation.writeObject(java.io.DataOutput)
readObject(GeneiousObjectInputStream) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Reconstructs this sequence from data previously created using SequenceCharSequence.writeObject(GeneiousObjectOutputStream , jebl.util.ProgressListener)
readObject(DataInput) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Reconstructs this sequence from data previously created using SequenceCharSequence.writeObject(java.io.DataOutput, jebl.util.ProgressListener)
readObject(GeneiousObjectInputStream) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Recreates a sequence from a stream previously written to using DefaultSequenceDocument.writeObject(com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectOutputStream , jebl.util.ProgressListener)
readObject(DataInput) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Recreates a sequence from a stream previously written to using DefaultSequenceDocument.writeObject(java.io.DataOutput, jebl.util.ProgressListener)
readObject(PluginDocument, DataInput) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Reads this object from a DataInput.
readSequence() - Method in class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectInputStream: Reads a sequence from this input stream that was previously written using GeneiousObjectOutputStream.writeSequence(SequenceDocument, jebl.util.ProgressListener)
readSequence(DataInput) - Static method in class com.biomatters.geneious.publicapi.utilities.DataInputOutputUtilities: Reads a sequence from this input stream that was previously written using DataInputOutputUtilities.writeSequence(java.io.DataOutput, com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument ,jebl.util.ProgressListener)
readUTF() - Method in class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectInputStream
readUTF(DataInput) - Static method in class com.biomatters.geneious.publicapi.utilities.DataInputOutputUtilities: Reads UTF (previously written by DataInputOutputUtilities.writeUTF(java.io.DataOutput, String)) from a DataInput without running into the 65K limit normally encountered with DataInput.readUTF()
readXmlSerializable(DataInput) - Static method in class com.biomatters.geneious.publicapi.utilities.DataInputOutputUtilities: Reads an XMLSerializable from this input stream that was previously written using DataInputOutputUtilities.writeXmlSerializable(java.io.DataOutput, com.biomatters.geneious.publicapi.documents.XMLSerializable, jebl.util.ProgressListener)
RECOGNITION_PATTERN - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Name to use for SequenceAnnotationQualifiers that specify the recognition pattern of a restriction enzyme.
REFERENCE_SEQUENCE_NAME - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The name of the reference sequence (if any) in an alignment or contig.
REFERENCE_UNIQUE_ID_SUFFIX - Static variable in class com.biomatters.geneious.publicapi.plugin.Assembler: If an assembly implementation supports both reference sequence and de novo assembly, its referenced assembler Assembler.getUniqueId() should end with this.
REFERENCED_DOCUMENT_LABEL_PREFIX - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: If a qualifier starts with either SequenceAnnotationQualifier.WEAK_REFERENCED_DOCUMENT_PREFIX or SequenceAnnotationQualifier.STRONG_REFERENCED_DOCUMENT_PREFIX then in may optionally contain a label to display to the user assoicated with the link by appending this suffix after the URN of the document followed by the text to display to the user.
RELATIVE_POSITION_BELOW - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: Added to the position of a statistic to position it below the other statistic.
RELATIVE_POSITION_DIRECTLY_BELOW - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: Added to the position of a statistic to position it directly below the other statistic.
remove(AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: Remove a document previously added using RetrieveCallback.add(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument,java.util.Map).
remove(E) - Method in class com.biomatters.geneious.publicapi.utilities.WeakReferenceList: Removes a reference to an object previously added using WeakReferenceList.add(Object).
remove(SimpleListener) - Method in class com.biomatters.geneious.publicapi.utilities.WeakSimpleListenerManager
removeAction(GeneiousAction) - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: Remove an action from the toolbar, the button associated with the action will be removed.
removeActionListener(ActionListener) - Method in class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption: Removes a listener added using Options.ButtonOption.addActionListener(java.awt.event.ActionListener).
removeActionsChangedListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.ActionProvider: removes a listener added using addActionsChangedListener
removeActiveOptionsChangedListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.PluginPreferences: Removes a listener previously added using PluginPreferences.addActiveOptionsChangedListener(org.virion.jam.util.SimpleListener)
removeAdditionalAction(GeneiousAction) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Removes an additional action (added previously using WritableDatabaseService.addAdditionalAction(com.biomatters.geneious.publicapi.plugin.GeneiousAction)) that this service provides.
removeAdditionalHelp(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Removed some additional help added using WritableDatabaseService.addAdditionalHelp(String)
removeAll() - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar
removeAll() - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel
removeAllItems() - Method in class com.biomatters.geneious.publicapi.components.GComboBox
removeAminoAcidSequence(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
removeAminoAcidSequence(int) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceListDocument: Removes the amino acid sequence at the given index from this sequence list and shifts any subsequent sequences to the left (subtracts one from their indices).
removeChangeListener(ChangeListener) - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: Remove a listener from the list of listeners.
removeChangeListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.FolderView: Remove a listener added using FolderView.addChangeListener(org.virion.jam.util.SimpleListener).
removeChangeListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Remove a change listener added using DocumentNoteField.addChangeListener(org.virion.jam.util.SimpleListener).
removeChangeListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousPreference: Deprecated.
removeChangeListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions: Removes a listener previously added using Options.MultipleOptions.addChangeListener(org.virion.jam.util.SimpleListener).
removeChangeListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: remove a listener to be notified when the value of this option changes
removeChangeListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Remove a listener to be notified when the value of any option changes
removeChildFolder(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Removes a child folder with this folder name.
removeChildFolder(String, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Removes a child folder with this folder name.
removeDatabase(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService: Remove the database with the given uniqueID (returned from GeneiousService.getUniqueID()).
removeDatabase(String, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService: Remove the database with the given uniqueID (returned from GeneiousService.getUniqueID()).
removeDatabaseServiceListener(DatabaseServiceListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: Remove a listener which was added using DatabaseService.addDatabaseServiceListener(DatabaseServiceListener) or DatabaseService.addWeakDatabaseServiceListener(DatabaseServiceListener)
.
removeDatabaseServiceListener(DatabaseServiceListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: A sub-class must not override this, but should instead use WritableDatabaseService.getDatabaseServiceListeners() as this class relies on WritableDatabaseService.getDatabaseServiceListeners().
removeDefaultsRestoredListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Remove a listener to be notified when the options are restored to their defaults (e.g.
removeDocument(AnnotatedPluginDocument, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Remove a document from this database.
removeDocumentProperties(URN) - Method in class com.biomatters.geneious.publicapi.databaseservice.FolderView: Removes any properties associated with this document.
removeFeedbackAction(String) - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame
removeFeedbackAction(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback
removeField(String) - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType: Remove a field.
removeGaps() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Creates a new sequence identical to this once except all gaps (both end and internal) have been removed.
removeGaps() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
removeGaps(SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Equivalent to calling removeGaps(sequence, true)
removeGaps(SequenceDocument, boolean) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: creates a sequence the same as the given sequence but with gap characters removed.
removeGaps(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Constructs a sequence without gaps ('-') from a specified sequence that potentially has gaps.
removeGeneiousServiceListener(GeneiousServiceListener) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Remove a listener to be notified about changes to this service.
removeHiddenElement(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: removes a hidden element.
removeInterval(SequenceAnnotationInterval) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Removes the given interval from this annotation.
removeInvalidResidues(CharSequence, SequenceType, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Get a sequence string identical to sequence except that any invalid residues are removed.
removeItem(Object) - Method in class com.biomatters.geneious.publicapi.components.GComboBox
removeItemAt(int) - Method in class com.biomatters.geneious.publicapi.components.GComboBox
removeLicenseTypeChangeListener(SimpleListener) - Static method in class com.biomatters.geneious.publicapi.plugin.License: Removes a listener added using addLicenseTypeChangeListener()
removeNote(String) - Method in interface com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.DocumentNotes: Remove a note from this AnnotatedPluginDocument
removeNucleotideSequence(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
removeNucleotideSequence(int) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceListDocument: Removes the nucleotide sequence at the given index from this sequence list and shifts any subsequent sequences to the left (subtracts one from their indices).
removeOutputDocument(URN) - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument: Removes an output document from the record.
removeOverlayIcons(Icons) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: remove an icon added using WritableDatabaseService.addOverlayIcons(com.biomatters.geneious.publicapi.plugin.Icons)
removePluginChangedListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin: Remove a listener previously added using GeneiousPlugin.addPluginChangedListener(org.virion.jam.util.SimpleListener).
removeProgressListener(ProgressListener) - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame: Removes a listener added using ProgressFrame.addProgressListener(jebl.util.ProgressListener)
removeQualifier(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Deletes all existing qualifiers with the given name
removeQualifier(SequenceAnnotationQualifier) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Removes the given qualifier from this annotation.
removeSearchCancelledListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: Remove a listener to be notified when a search on this database has been cancelled
removeSearchResultPropertiesAdjuster(WritableDatabaseService.SearchResultPropertiesAdjuster) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Removed a SearchResultPropertiesAdjuster added via WritableDatabaseService.addSearchResultPropertiesAdjuster(com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService.SearchResultPropertiesAdjuster).
removeSequence(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Removes the specified sequence from the alignment.
removeSequence(int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
removeSequence(int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
removeSequence(int) - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Removes a sequence from this PairedReadManager, unpairing it with its mate if necessary.
removeSequence(int) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
removeShortcutChangeListener(GeneiousActionOptions.ShortcutChangeListener) - Static method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Remove a shortcut change listener
removeStateChangeListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.components.MoreOptionsButton: Remove a state change listener.
removeStreamHandler(String, URLStreamHandler) - Static method in class com.biomatters.geneious.publicapi.plugin.URLStreamHandlerManager: Deprecated.
Do not call
removeSubMenuActionsChangedListener(SimpleListener) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction.SubMenu: Remove a SubMenuActionsChangedListener
removeTrack(SequenceTrack) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Removes an existing track.
removeTreeChangedListener(TreeChangeListener) - Method in class com.biomatters.geneious.publicapi.plugin.TreeViewerExtension: Remove a listener previously added using TreeViewerExtension.addTreeChangedListener(jebl.evolution.trees.TreeChangeListener).
removeValue(Options) - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions: Removes one of the multiple options terms.
removeWeakLicenseTypeChangeListener(SimpleListener) - Static method in class com.biomatters.geneious.publicapi.plugin.License: Removes a listener added using License.addWeakLicenseTypeChangeListener(org.virion.jam.util.SimpleListener)
removeWeakReferenceDocumentListener(DocumentListener) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Remove a listener previously added using AnnotatedPluginDocument.addWeakReferenceDocumentListener(DocumentListener).
removeWritableDatabaseServiceRootListener(PluginUtilities.WritableDatabaseServicesListener) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: Remove a listener previously added using addLocalDatabaseSevicesListener
removeZoomToSelectionActionListener(ActionListener) - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel
Renamable - Interface in com.biomatters.geneious.publicapi.documents: Provides that ability to rename something.
renameFolder(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Rename this folder.
renameToWithRetry(File, File) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Similar to File.renameTo(java.io.File) except that if the rename fails, we retry a few times (performing garbage collections and sleeping briefly between attempts) if necessary until it succeeds, potentially waiting for up to approximately 1 second.
reorder(List<T>, int[]) - Static method in class com.biomatters.geneious.publicapi.utilities.GeneralUtilities: adjusts the ordering of elements in the array according to the ordering array.
reorder(int[], int[]) - Static method in class com.biomatters.geneious.publicapi.utilities.GeneralUtilities: adjusts the ordering of elements in the array according to the ordering array.
reorder(char[], int[]) - Static method in class com.biomatters.geneious.publicapi.utilities.GeneralUtilities: adjusts the ordering of elements in the array according to the ordering array.
reorder(boolean[], int[]) - Static method in class com.biomatters.geneious.publicapi.utilities.GeneralUtilities: adjusts the ordering of elements in the array according to the ordering array.
reorder(BitSet, int[]) - Static method in class com.biomatters.geneious.publicapi.utilities.GeneralUtilities: adjusts the ordering of elements in the BitSet according to the ordering array.
reorder(byte[], int[]) - Static method in class com.biomatters.geneious.publicapi.utilities.GeneralUtilities: adjusts the ordering of elements in the array according to the ordering array.
reorderAminoAcidSequences(int[]) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
reorderAminoAcidSequences(int[]) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceListDocument: Adjusts the ordering of sequences in this list according to the ordering array.
reorderNucleotideSequences(int[]) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
reorderNucleotideSequences(int[]) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceListDocument: Adjusts the ordering of sequences in this list according to the ordering array.
reorderSequences(int[]) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Adjusts the ordering of sequences in the alignment according to the ordering array.
reorderSequences(int[]) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
reorderSequences(int[]) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
reorderSequences(int[]) - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Reorders the sequences in this paired read manager, as defined by GeneralUtilities.reorder(int[], int[]).
reorderSequences(int[]) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
repeatedCharSequence(CharSequence, int) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities: Create a CharSequence that repeats another CharSequence a given number of times.
replaceAminoAcidSequence(int, AminoAcidSequenceDocument) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
replaceAminoAcidSequence(int, AminoAcidSequenceDocument) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.ExtendedEditableSequenceListDocument: Replaces the amino acid sequence at this index with a new sequence.
replaceContents(DefaultSequenceListDocument) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: Copies all the sequence data from another DefaultSequenceListDocument into this document.
replaceInputDocument(URN, URN) - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument: Replaces the URN of an output document with a new one.
replaceNucleotideSequence(int, NucleotideSequenceDocument) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
replaceNucleotideSequence(int, NucleotideSequenceDocument) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.ExtendedEditableSequenceListDocument: Replaces the nucleotide sequence at this index with a new sequence.
replaceOutputDocument(URN, URN) - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument: Replaces the URN of an output document with a new one.
replaceQuestionMarksWithMaximalAmbiguitySymbol(SequenceType, String) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: get a version of a sequence string with any question marks replaces with N (for nucleotide sequences) or X (for protein sequences)
rerunOperation(ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument: Reruns an operation, replacing all output documents of the operation with their corresponding new document
reset() - Method in class com.biomatters.geneious.publicapi.utilities.ProgressInputStream: Overrides FilterInputStream.reset to reset the progress monitor as well as the stream.
resetAllDialogPreferences() - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Reset all the 'Don't ask again' and 'Remember my preference' so that the dialogs will be shown again.
resetDialogPreference(String) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: If the user has previously chosen 'dont ask again' or 'remember my preference' for the given preference key, then reset it.
restoreDefault() - Method in class com.biomatters.geneious.publicapi.plugin.Options.EditableComboBoxOption
restoreDefault() - Method in class com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption
restoreDefault() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Restore this option to its default value
restoreDefaults() - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions: Restores these MultipleOptions to their default value (i.e.
restoreDefaults() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Restores all current option values and child options to their default values.
restorePreferences() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Restore the current option values from the default persistent storage location by calling restorePreferences(null, false)
Note: If there is no value for an option in preferences then it value isn't changed by this method.
restorePreferences(String, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Restores the current option values from persistent storage, i.e.
restrictedName(boolean) - Static method in class com.biomatters.geneious.publicapi.plugin.License: The word used to describe Geneious when it doesn't have an active license.
resumeSearch(String, RetrieveCallback) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: Deprecated.
Geneious no longer supports resuming searches
retrieve(Query, RetrieveCallback, URN[]) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: Get documents by searching a database.
retrieve(AnnotatedPluginDocument[], RetrieveCallback, URN[]) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: Retrieves full documents corresponding to the given summary documents from the database.
retrieve(URN[], RetrieveCallback) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: Retrieve documents with the specified URNs.
retrieve(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: Convenience method to be used instead of the standard retrieve method when doing a standard textbased search and ignoring failure (by returning an empty list) and ignoring search properties (such as e-values).
retrieve(Query, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: Convenience method to be used instead of the standard DatabaseService.retrieve(Query, RetrieveCallback, com.biomatters.geneious.publicapi.documents.URN[]) method to avoid dealing with a callback method.
retrieve(List<AnnotatedPluginDocument>, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: Convenience method to be used instead of the standard retrieve method to avoid dealing with a callback method when downloading full documents given summary documents.
retrieve(AnnotatedPluginDocument[], RetrieveCallback, URN[]) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService
retrieve(URN[], RetrieveCallback) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService
retrieve(Query, RetrieveCallback, URN[]) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService
RetrieveCallback - Class in com.biomatters.geneious.publicapi.databaseservice: A callback that asynchronously reports back the documents resulting from a DatabaseService search.
RetrieveCallback(RetrieveCallback) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: Creates a wrapper callback that delegates all non-overriden methods to an internal callback class.
RetrieveCallback(ProgressListener) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: Creates a wrapper callback that delegates all non-overriden ProgressListener methods to an internal ProgressListener.
RetrieveCallback() - Constructor for class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: Default constructor.
reverse() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Create a new sequence that is the reverse of this sequence.
reverse() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
reverse(int, SequenceDocument.Alphabet) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Creates a new annotation that is either the reverse or the reverse complements this annotation.
reverse() - Method in enum com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval.Direction: The opposite direction from this one, i.e.
reverse() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Deprecated.
use SequenceAnnotationInterval.getReverse() instead.
reverse(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities: Provides a reversed view onto the specified sequence.
reverse() - Method in class com.biomatters.geneious.publicapi.utilities.Interval
reverseComplement(NucleotideGraph) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Creates a new graph that is the reverse complement of the given graph.
reverseComplement() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Create a new sequence that is the reverse complement of this sequence.
reverseComplement() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
reverseComplement(SequenceDocument) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Convenience method for calling reverseComplement(sequenceToReverse,true).
reverseComplement(SequenceAlignmentDocument) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Creates a new alignment that is the reverse complement of the given alignment.
reverseComplement(SequenceDocument, boolean) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Create a sequence that is the reverse complement another sequence.
reverseComplement(SequenceDocument, boolean, boolean) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Create a sequence that is the reverse complement another sequence.
reverseComplement(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Provides a dynamic reverse complement view onto a nucletoide CharSequence.
REVERSED_NAME_SUFFIX - Static variable in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: The suffix that is appended to sequence names when they are reversed.
RIGHT - Static variable in class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption
ROOT_ELEMENT_NAME - Static variable in interface com.biomatters.geneious.publicapi.documents.XMLSerializable: The default root element name.
RootedTreeDocument - Interface in com.biomatters.geneious.publicapi.documents.types: A document containing one (rooted) tree.
run(int, int) - Method in class com.biomatters.geneious.publicapi.utilities.MultiThreadedTask: Runs a part of this task in a single thread.
run() - Method in class com.biomatters.geneious.publicapi.utilities.MultiThreadedTask: Creates threads, executes all the parts and waits for them to finish before returning.
runLocally(AnnotatedPluginDocument[], ProgressListener, Options, Options, String, DocumentOperation.OperationCallback) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: GeneiousGridDocumentOperations that support local runs must implement either this method or GeneiousGridDocumentOperation.runLocally(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], jebl.util.ProgressListener, Options, Options, String)
Performs a local run of the program, and adds any documents that are generated to an OperationCallback.
runLocally(AnnotatedPluginDocument[], ProgressListener, Options, Options, String) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: GeneiousGridDocumentOperations that support local runs must implement either this method or #runLocally(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], jebl.util.ProgressListener, Options, Options, String, OperationCallback)
Performs a local run of the program, and returns any documents that are generated.
runLocally(List<AnnotatedPluginDocument>, ProgressListener, Options, Options, String) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridDocumentOperation: GeneiousGridDocumentOperations that support local runs should implement this method.
RuntimeDocumentOperationException - Exception in com.biomatters.geneious.publicapi.plugin: Occasionally some methods that would like to throw a DocumentOperationException are unable to do so because their API doesn't allow it.
RuntimeDocumentOperationException(DocumentOperationException) - Constructor for exception com.biomatters.geneious.publicapi.plugin.RuntimeDocumentOperationException

S

safeEquals(T, T) - Static method in class com.biomatters.geneious.publicapi.utilities.GeneralUtilities: Safely checks whether two Objects are either equal (a.equals(b)) or both null, without ever throwing a NullPointerException.
SameTaxaTreesDocument - Interface in com.biomatters.geneious.publicapi.documents.types: A document containing a list of trees.
save() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Saves the document summary to the database.
save(boolean) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Saves the document summary to the database.
save() - Method in class com.biomatters.geneious.publicapi.documents.DocumentHistory: Saves the document history.
saveAdditionalPerDocumentXml(AnnotatedPluginDocument, String, boolean, Element, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Save some additional XML associated with a particular document.
saveAdditionalPerDocumentXml(AnnotatedPluginDocument, boolean, Map<String, ElementProvider>, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Save some additional XML associated with a particular document.
saveDocument(AnnotatedPluginDocument, boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: A document that is already in this database has been modified in memory and should now be saved to permanent storage.
saveDocument() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Saves the internal PluginDocument and the AnnotatedPluginDocument to the database.
saveDocument(AnnotatedPluginDocument.ActiveLinkSaveBehaviour, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Saves the internal PluginDocument and the AnnotatedPluginDocument to the database.
saveDocument(AnnotatedPluginDocument.ActiveLinkSaveBehaviour, boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Saves the internal PluginDocument and the AnnotatedPluginDocument to the database.
saveNotes() - Method in interface com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.DocumentNotes: Saves these notes to the AnnotatedPluginDocument and in turn to the database.
savePreferences(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Save the current option values persistently, i.e.
savePreferences() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Save the current option values persistently in the default storage location by calling savePreferences(null)
SEARCH_RESULTS_SERVICE_UNIQUE_ID - Static variable in class com.biomatters.geneious.publicapi.plugin.PluginUtilities: The unique ID of the local database root "Searches" service.
searchableStatusChanged(boolean, String) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseServiceListener: Notify using code about a change in status of searchability.
searchField - Variable in class com.biomatters.geneious.publicapi.documents.AdditionalSearchContent.Result: Field search for advanced search.
selectDocument(URN) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Changes the currently selected document in the Geneious document table.
selectDocuments(List<URN>) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Changes the currently selected documents in the Geneious document table.
selectDocuments(List<URN>, SequenceSelection) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Changes the currently selected documents in the Geneious document table and selects a region within them.
selectionClass - Variable in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature.DocumentSelectionSignatureAtom: Either an actual document class or one of the interfaces which a document may implement.
seqresAndAtomMatch(String) - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument: Whether the ATOM records in this chain have residue sequence numbers which correspond to the sequence given in the SEQRES section
SEQUENCE_COUNT - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The number of sequences in an alignment or set of sequences.
SEQUENCE_DIRECTION - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Deprecated.
no longer used by binning, replaced by DocumentField.BINNING_FRAME
SEQUENCE_LENGTH - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The number of residues or bases in a sequence or the length of an alignment.
SEQUENCE_LIST_ORDERING_REVISION_NUMBER - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: A cache of the value returned from EditableSequenceListDocument.getOrderingRevisionNumber()
All EditableSequenceListDocuments created in Geneious 6.0.5 or later have this field.
SEQUENCE_LIST_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: Sequence list document type which matches either nucleotide or protein sequence lists.
SEQUENCE_SEARCH_AMINO_ACID_HIT - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: CombinedAlignmentAndAminoAcidSequenceDocument document type
SEQUENCE_SEARCH_NUCLEOTIDE_HIT - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: CombinedAlignmentAndNucleotideSequenceDocument document type
SEQUENCE_TYPE - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Allows marking of special types of sequence like vectors and references.
SEQUENCE_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: SequenceDocument document type
SequenceAlignmentDocument - Class in com.biomatters.geneious.publicapi.documents.sequence: An alignment or contig of sequences.
SequenceAlignmentDocument() - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument
SequenceAlignmentDocument.ReferencedSequence - Class in com.biomatters.geneious.publicapi.documents.sequence: Represents a reference to the original document that a sequence in this alignment was aligned from.
SequenceAlignmentDocument.ReferencedSequence(AnnotatedPluginDocument, int) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument.ReferencedSequence
SequenceAlignmentDocument.ReferencedSequence(AnnotatedPluginDocument) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument.ReferencedSequence: Construct a reference to a document that is a SequenceDocument.
SequenceAlignmentListDocument - Interface in com.biomatters.geneious.publicapi.documents.sequence: A document representing a list of alignments.
SequenceAnnotation - Class in com.biomatters.geneious.publicapi.documents.sequence: Provides information on a subset of the sequence.
SequenceAnnotation(String, String) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Constructs a new SequenceAnnotation with the specified name and type.
SequenceAnnotation(String, String, SequenceAnnotationInterval...) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Constructs a new SequenceAnnotation with the specified name and type.
SequenceAnnotation(Element) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: XML deserialization constructor.
SequenceAnnotation(SequenceAnnotation) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: creates a copy of the given annotation
SequenceAnnotation(SequenceAnnotation, int) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: creates a copy of the given annotation offset by a certain amount
SequenceAnnotationGenerator - Class in com.biomatters.geneious.publicapi.plugin: A SequenceAnnotationGenerator generates annotations on a sequence, set of sequences, or an alignment.
SequenceAnnotationGenerator() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator
SequenceAnnotationGenerator.AnnotationGeneratorResult - Class in com.biomatters.geneious.publicapi.plugin: Represents the result of a single sequence from calling an annotation generator via SequenceAnnotationGenerator.generate(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange, jebl.util.ProgressListener, Options)
SequenceAnnotationGenerator.AnnotationGeneratorResult() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Constructs a new AnnotationGeneratorResult with no results.
SequenceAnnotationGenerator.AnnotationGeneratorResult(List<SequenceAnnotation>) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult: Constructs a new AnnotationGeneratorResult
SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment - Class in com.biomatters.geneious.publicapi.plugin: An immutable class representing an insertion, deletion, or replacement of residues or bases in a sequence.
SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment(int, int, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment: Construct a new insertion, deletion, or replacement of residues or bases in a sequence.
SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment(ImmutableSequence) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment: Replaces the entire sequence with a new sequence.
SequenceAnnotationGenerator.AnnotationGeneratorResultOnAlignment - Class in com.biomatters.geneious.publicapi.plugin: Represents the results of running a generator on a single alignment.
SequenceAnnotationGenerator.AnnotationGeneratorResultOnAlignment(List<SequenceAnnotationGenerator.AnnotationGeneratorResult>) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResultOnAlignment: Constructs a new AnnotationGeneratorResultOnAlignment.
SequenceAnnotationGenerator.AnnotationGeneratorResultsOnSingleSequence - Class in com.biomatters.geneious.publicapi.plugin: An implementation of a List of SequenceAnnotationGenerator.AnnotationGeneratorResult where all elements except one are empty results.
SequenceAnnotationGenerator.AnnotationGeneratorResultsOnSingleSequence(int, int, SequenceAnnotationGenerator.AnnotationGeneratorResult) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResultsOnSingleSequence
SequenceAnnotationGenerator.SelectionGrabOption - Class in com.biomatters.geneious.publicapi.plugin: If any option returned from SequenceAnnotationGenerator.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange) is a SelectionGrabOption then the sequence viewer will interact with the option such that when the user clicks on the button representing this option, the current selection in the sequence viewer is copied to this option value.
SequenceAnnotationGenerator.SelectionGrabOption(String, Interval) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionGrabOption: Constructs a new SelectionGrabOption
SequenceAnnotationGenerator.SelectionGrabOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionGrabOption
SequenceAnnotationGenerator.SelectionRange - Class in com.biomatters.geneious.publicapi.plugin: represents a rectangular selection range in a list of sequences, and also behaves like a Linked List in that it provides a link to the next SelectionRange in a chain of selections (see SequenceAnnotationGenerator.SelectionRange.getNext().
SequenceAnnotationGenerator.SelectionRange(int, int, int, int) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange
SequenceAnnotationGenerator.SelectionRange(int, int, int, int, SequenceAnnotationGenerator.SelectionRange) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange
SequenceAnnotationGenerator.SingleSequenceResultGenerator - Class in com.biomatters.geneious.publicapi.plugin: Provides a system for a SequenceAnnotationGenerator to generate results for just a single sequence.
SequenceAnnotationGenerator.SingleSequenceResultGenerator() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SingleSequenceResultGenerator
SequenceAnnotationGroup - Class in com.biomatters.geneious.publicapi.documents.sequence: An immutable class representing a collection of related SequenceAnnotation types.
SequenceAnnotationGroup(String, String...) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup: construct a new SequenceAnnotationGroup with the specified name and types
SequenceAnnotationInterval - Class in com.biomatters.geneious.publicapi.documents.sequence: Immutable pair of integers with a direction, representing a directed range in the sequence annotation.
SequenceAnnotationInterval(String) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: constructs interval from the string representation of the form "[...]n,nnn D m,mmm[...]" where "n,nnn" is an integer with commas every three digits and "D" is a valid direction (see SequenceAnnotationInterval.Direction.toArrowString()).
SequenceAnnotationInterval(Interval) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Creates a SequenceAnnotationInterval (which uses 1-based inclusive max co-ordinates) from an interval (which uses 0-based exclusive max co-ordinates)
SequenceAnnotationInterval(int, int) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Backwards compatibility constructor for an interval that starts at index from (inclusive) and ends at index to (inclusive).
SequenceAnnotationInterval(int, int, SequenceAnnotationInterval.Direction) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval
SequenceAnnotationInterval(int, int, SequenceAnnotationInterval.Direction, boolean, boolean) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Main constructor.
SequenceAnnotationInterval(SequenceAnnotationInterval) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Construct a SequenceAnnotationInterval that is identical to the given parameter.
SequenceAnnotationInterval.Direction - Enum in com.biomatters.geneious.publicapi.documents.sequence: The direction of a sequence annotation interval.
SequenceAnnotationQualifier - Class in com.biomatters.geneious.publicapi.documents.sequence: A named item of information (i.e.
SequenceAnnotationQualifier(String, String) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: create a new SequenceAnnotationQualifier
SequenceAnnotationQualifier(SequenceAnnotationQualifier) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: creates a copy of the given SequenceAnnotationQualifier.
SequenceAnnotationQualifier(String, URN, boolean, String) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: create a new SequenceAnnotationQualifier which contains a reference to another document.
sequenceAnnotationsToXML(String, List<SequenceAnnotation>) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Return a list of sequence annotations as XML.
sequenceAnnotationsToXML(Geneious.MajorVersion, String, List<SequenceAnnotation>) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Return a list of sequence annotations as XML in the specified version of Geneious
SequenceBuilder - Class in com.biomatters.geneious.publicapi.documents.sequence: Provides methods for creating CharSequences for use as biological sequences.
SequenceBuilder() - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceBuilder
SequenceCharSequence - Class in com.biomatters.geneious.publicapi.documents.sequence: A CharSequence that knows the length of its terminal gaps (sequences of '-') and allows for efficient insertions and deletions of subsequences.
SequenceDatabaseSuperService - Class in com.biomatters.geneious.publicapi.databaseservice: A plugin should return a service which extends this class if it wishes to provide a Sequence Search facility that can have databases added and removed by the user or if there are some general preferences that apply to the Sequence Datbases of the plugin.
SequenceDatabaseSuperService() - Constructor for class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService
SequenceDocument - Interface in com.biomatters.geneious.publicapi.documents.sequence: Interface representing one sequence.
SequenceDocument.Alphabet - Enum in com.biomatters.geneious.publicapi.documents.sequence: Supported sequence types.
SequenceDocument.Transformer - Class in com.biomatters.geneious.publicapi.documents.sequence: Provides a method for returning a new sequence which represents a transformation made to another sequence.
SequenceDocument.Transformer() - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument.Transformer
SequenceDocumentWithEditableAnnotations - Interface in com.biomatters.geneious.publicapi.documents.sequence: An extension of a SequenceDocument that allows its annotations to be changed.
SequenceExtractionUtilities - Class in com.biomatters.geneious.publicapi.implementations: Provides methods for extracting a portion of a sequence to a new sequence document.
SequenceExtractionUtilities.ExtractionOptions - Class in com.biomatters.geneious.publicapi.implementations: Represents options controling how sequence extraction works in SequenceExtractionUtilities.extractIntervals(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions).
SequenceExtractionUtilities.ExtractionOptions(SequenceExtractionUtilities.ExtractionOptions) - Constructor for class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Constructs some new extraction options identical to the given ones.
SequenceExtractionUtilities.ExtractionOptions(int, int) - Constructor for class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Construct the extraction options with a single interval from extractFrom to extractTo inclusive.
SequenceExtractionUtilities.ExtractionOptions(List<SequenceAnnotationInterval>) - Constructor for class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Construct the extraction options from a list of intervals.
SequenceExtractionUtilities.ExtractionOptions(SequenceAnnotationInterval...) - Constructor for class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Construct the extraction options from a list of intervals.
SequenceExtractionUtilities.ExtractionOptions(Interval...) - Constructor for class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Construct the extraction options from a list of intervals.
SequenceGapInformation - Class in com.biomatters.geneious.publicapi.implementations: Precalculates information about the location of gaps ('-') in a CharSequence, and can efficiently calculate translate between indices in the gapped and ungapped sequence.
SequenceGapInformation(Element, SequenceCharSequence) - Constructor for class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Deserializes a SequenceGapInformation from XML previously returned from SequenceGapInformation.toXML(String).
SequenceGapInformation(CharSequence) - Constructor for class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Constructs SequenceGapInformation for the specified gapped sequence.
SequenceGapInformation(CharSequence, ProgressListener) - Constructor for class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Constructs SequenceGapInformation for the specified gapped sequence.
SequenceGapInformation.Provider - Interface in com.biomatters.geneious.publicapi.implementations: An interface that SequenceDocuments can optionally to implement to indicate they may provide a (potentially) pre-built SequenceGapInformation
SequenceGraph - Class in com.biomatters.geneious.publicapi.plugin: A sequence graph is displayed in the SequenceViewer.
SequenceGraph() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceGraph
SequenceGraph.Location - Enum in com.biomatters.geneious.publicapi.plugin
SequenceGraph.SequencePropertyRetriever - Class in com.biomatters.geneious.publicapi.plugin: Provides additional information about the sequence(s) (e.g.
SequenceGraph.SequencePropertyRetriever() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceGraph.SequencePropertyRetriever
SequenceGraphFactory - Class in com.biomatters.geneious.publicapi.plugin: A sequence graph factory is used for creating instances of SequenceGraphs every time a new document is viewed in the sequence viewer.
SequenceGraphFactory() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceGraphFactory
SequenceListDocument - Interface in com.biomatters.geneious.publicapi.documents.sequence: A document containing 0 or more nucleotide and 0 or more protein sequences.
SequenceListOnDisk<T extends SequenceDocument> - Class in com.biomatters.geneious.publicapi.documents.sequence: A list of sequences which are loaded from disk on demand rather than all stored in memory.
SequenceListOnDisk.AlignmentData - Class in com.biomatters.geneious.publicapi.documents.sequence: An immutable class (all of whose elements are immutable too) representing the sequences and data relevant to the sequences (excluding the reference sequence) in an alignment.
SequenceListOnDisk.AlignmentData(Element) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.AlignmentData: Recreates AlignmentData from a previously serialized AlignmentData
SequenceListOnDisk.Builder<T extends SequenceDocument> - Class in com.biomatters.geneious.publicapi.documents.sequence: Used for building a SequenceListOnDisk.
SequenceListOnDisk.Builder(boolean, SequenceDocument.Alphabet, boolean) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Create a new builder
SequenceListOnDisk.Builder(boolean, SequenceDocument.Alphabet, boolean, ProgressListener, int) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Create a new builder
SequenceListOnDisk.Builder(boolean, SequenceDocument.Alphabet, boolean, ProgressListener, int, boolean) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Create a new builder
SequenceListSummary - Class in com.biomatters.geneious.publicapi.documents.sequence: Provides a summary of data in a list of sequences.
SequenceListSummary(SequenceDocument.Alphabet, int) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Constructs a new summary.
SequenceListSummary(SequenceDocument.Alphabet, int, int) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Constructs a new summary.
SequenceListSummary(SequenceDocument.Alphabet, int, int, boolean) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary
SequenceListSummary(SequenceListSummary, SequenceListSummary) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Constructs a new SequenceListSummary by combining 2 other summaries.
SequenceListSummary(List<SequenceDocument>, boolean, ProgressListener) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: A convenience constructor which just calls SequenceListSummary.addSequence(SequenceDocument) for each sequence in the list and then calls SequenceListSummary.finishedAddingSequences(jebl.util.ProgressListener)
SequenceListSummary(Element) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary: Creates a summary from a previously serialized summary
SequenceListSummary.Coverage - Class in com.biomatters.geneious.publicapi.documents.sequence: Represents the coverage (number of sequences covering a column in an alignment)
SequenceListSummary.Coverage(double, int, int, boolean) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Coverage
SequenceListSummary.Coverage(double, double, double, boolean) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Coverage
SequenceListSummary.PairwiseSimilarity - Class in com.biomatters.geneious.publicapi.documents.sequence: Immutable value class representing the number of identical and non-identical pairs of bases/residues in an alignment column.
SequenceListSummary.PairwiseSimilarity(SequenceListSummary.PairwiseSimilarity, SequenceListSummary.PairwiseSimilarity) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.PairwiseSimilarity: Constructs a new PairwiseSimilarity by adding 2 PairwiseSimilarities together
SequenceListSummary.PairwiseSimilarity(double, long, long, long) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.PairwiseSimilarity: Constructs a new PairwiseSimilarity
SequenceListSummary.PairwiseSimilarity(Element) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.PairwiseSimilarity: Recreates a PairwiseSimilarity from XML previously returned from SequenceListSummary.PairwiseSimilarity.toXML(String)
SequenceListSummary.Provider - Interface in com.biomatters.geneious.publicapi.documents.sequence: An interface that lists of sequences (e.g.
SequencePropertiesStorage - Class in com.biomatters.geneious.publicapi.implementations.sequence: Provides supporting functionality for sequence classes that need to store various sequence properties and serialise those to XML.
SequencePropertiesStorage() - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: Default constructor with no arguments.
SequencePropertiesStorage(Element) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: Constructs a SequencePropertiesStorage object from a JDOM XML Element.
sequenceSearch(AnnotatedPluginDocument, String, Options, RetrieveCallback) - Method in class com.biomatters.geneious.publicapi.databaseservice.DatabaseService: If this is a Sequence Database (ie.
SequenceSelection - Class in com.biomatters.geneious.publicapi.plugin: Specifies a selection of regions in a sequence, list of sequences, alignment or other sequence containing document.
SequenceSelection(List<SequenceSelection.SelectionInterval>) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelection: Create a SequenceSelection
SequenceSelection(SequenceSelection.SelectionInterval...) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelection: Create a SequenceSelection
SequenceSelection(SequenceSelection.SequenceIndex, SequenceAnnotation) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelection: Construct for a selected SequenceAnnotation on the specified sequence.
SequenceSelection(SequenceDocument, SequenceAnnotation) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelection: Deprecated.
use SequenceSelection.SequenceSelection(com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex, com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation) instead
SequenceSelection(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelection: Construct a SequenceSelection from the results of SequenceSelection.toXML()
SequenceSelection.SelectionInterval - Class in com.biomatters.geneious.publicapi.plugin: A contiguous selection of residues in a sequence.
SequenceSelection.SelectionInterval(int, int, SequenceDocument) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval: Deprecated.
use #SelectionInterval(SequenceIndex, int, int) instead
SequenceSelection.SelectionInterval(SequenceSelection.SequenceIndex, int, int) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
SequenceSelection.SelectionInterval(Interval, Interval, SequenceType, SequenceSelection.SequenceDocumentType) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval: Constructs a rectangular selection (i.e.
SequenceSelection.SelectionInterval(Interval, SequenceDocument) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval: Deprecated.
use #SelectionInterval(SequenceIndex, com.biomatters.geneious.publicapi.utilities.Interval) instead
SequenceSelection.SelectionInterval(SequenceSelection.SequenceIndex, Interval) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
SequenceSelection.SelectionInterval(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
SequenceSelection.SequenceDocumentType - Enum in com.biomatters.geneious.publicapi.plugin: Used for identifying the type of view the selection applies for identifying which list the index applies to in a CombinedAlignmentAndSequenceDocument
SequenceSelection.SequenceIndex - Class in com.biomatters.geneious.publicapi.plugin: Represents the index of the selected sequence and the type (so that we can identify which list the index applies to in SequenceListDocuments.
SequenceSelection.SequenceIndex(int, SequenceType, SequenceSelection.SequenceDocumentType) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex: Creates a new SequenceIndex
SequenceSelection.SequenceIndex(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex: Reconstruct using results returned from SequenceSelection.SequenceIndex.toXML()
SequenceSelection.SequenceIndex.SelectionWrongForDocumentsException - Exception in com.biomatters.geneious.publicapi.plugin: Deprecated.
use SequenceSelectionWithDocuments.SelectedDocumentsModifiedException instead
SequenceSelectionWithDocuments - Class in com.biomatters.geneious.publicapi.plugin: This class associates a SequenceSelection with the List of AnnotatedPluginDocument that it is defined on.
SequenceSelectionWithDocuments(List<AnnotatedPluginDocument>, SequenceSelection) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments: Invokes SequenceSelectionWithDocuments.SequenceSelectionWithDocuments(java.util.List, SequenceSelection, com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.ExtractionStrategy) with SequenceSelectionWithDocuments.DEFAULT_EXTRACTION_STRATEGY.
SequenceSelectionWithDocuments(List<AnnotatedPluginDocument>, SequenceSelection, SequenceSelectionWithDocuments.ExtractionStrategy) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments: Constructs an SequenceSelectionWithDocuments for the given documents and given SelectionSelection on those documents.
SequenceSelectionWithDocuments(List<AnnotatedPluginDocument>) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments: Invokes SequenceSelectionWithDocuments.SequenceSelectionWithDocuments(java.util.List, ExtractionStrategy) with SequenceSelectionWithDocuments.DEFAULT_EXTRACTION_STRATEGY.
SequenceSelectionWithDocuments(List<AnnotatedPluginDocument>, SequenceSelectionWithDocuments.ExtractionStrategy) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments: Constructor which "selects all" from the given documents.
It infers the SequenceType and SequenceSelection.SequenceDocumentType from the documents.
If the documents contain a mixture of nucleotide and amino acid sequences, this will throw an DocumentsInvalidException.
SequenceSelectionWithDocuments(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments: Construct a SequenceSelectionWithDocuments from the results of SequenceSelectionWithDocuments.toXML()
SequenceSelectionWithDocuments.DocumentsInvalidException - Exception in com.biomatters.geneious.publicapi.plugin: Thrown to indicate that a group of documents is not valid to have a SequenceSelectionWithDocuments upon.
SequenceSelectionWithDocuments.DocumentsInvalidException(String) - Constructor for exception com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.DocumentsInvalidException: Constructs a new instance of this exception with the given message
SequenceSelectionWithDocuments.ExtractionStrategy - Class in com.biomatters.geneious.publicapi.plugin: Instances of this allow calling code to fine tune how SequenceSelectionWithDocuments.getSequences() returns SequenceDocuments from its selection and documents.
SequenceSelectionWithDocuments.ExtractionStrategy() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.ExtractionStrategy
SequenceSelectionWithDocuments.SelectedDocumentsModifiedException - Exception in com.biomatters.geneious.publicapi.plugin: Thrown when the selected documents are modified between the moment when the SequenceSelectionWithDocuments is constructed and the documents within it are accessed.
SequenceSelectionWithDocuments.SelectedDocumentsModifiedException(String) - Constructor for exception com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.SelectedDocumentsModifiedException: Constructs a SelectedDocumentsModifiedException with the specified detail message.
SequenceTrack - Class in com.biomatters.geneious.publicapi.implementations.sequence: A Sequence Track is a list of annotations that is associated with a sequence (in addition to those supplied by SequenceDocument.getSequenceAnnotations()).
SequenceTrack(Element) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Deserializes a track from XML.
SequenceTrack(String) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Creates a new SequenceTrack.
SequenceTrack.Manager - Class in com.biomatters.geneious.publicapi.implementations.sequence: Manages all the tracks on a single sequence, including allowing tracks to added or removed.
SequenceTrack.Manager(PluginDocument) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Constructs a new empty manager with no tracks.
SequenceTrack.Manager(PluginDocument, Element) - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Recreates a manager from XML.
SequenceTrack.Manager.Provider - Interface in com.biomatters.geneious.publicapi.implementations.sequence: An interface implemented by SequenceDocuments or SequenceAlignmentDocuments to indicate they provide sequence tracks.
SequenceUtilities - Class in com.biomatters.geneious.publicapi.utilities: A noninstantiable class providing static methods for common tasks associated with nucleotide and protein sequences.
SequenceViewerExtension - Class in com.biomatters.geneious.publicapi.plugin: An extension which provides extra functionality in the sequence/alignment/contig viewer.
SequenceViewerExtension() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension
SequenceViewerExtension.ComponentLocation - Enum in com.biomatters.geneious.publicapi.plugin: A location in the sequence viewer for the component returned from SequenceViewerExtension.createComponent() specified by SequenceViewerExtension.getComponentLocation()
SequenceViewerExtension.Factory - Class in com.biomatters.geneious.publicapi.plugin: A type of plugin for creating extensions to the sequence viewer returned from GeneiousPlugin.getSequenceViewerExtensionFactories()
SequenceViewerExtension.Factory() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.Factory
SequenceViewerExtension.PropertyRetrieverAndEditor - Class in com.biomatters.geneious.publicapi.plugin: Provides methods for querying the sequence viewer about the status of various things and for requesting that the sequence viewer change its state.
SequenceViewerExtension.PropertyRetrieverAndEditor() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor
SequenceViewerExtension.PropertyRetrieverAndEditor.DiscardReferencesCallback - Interface in com.biomatters.geneious.publicapi.plugin: Used for indicating that references to values returned from PropertyRetrieverAndEditor#getVisibleAnnotations(PropertyRetrieverAndEditor.DiscardReferencesCallback) must be discarded.
SequenceViewerExtension.SequenceAnnotationWrapper - Class in com.biomatters.geneious.publicapi.plugin: Wraps a SequenceAnnotation and provides extra information about the location (sequence, track) of the annotation.
SequenceViewerExtension.SequenceAnnotationWrapper() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.SequenceAnnotationWrapper
SequenceViewerExtension.StatisticsFactory - Class in com.biomatters.geneious.publicapi.plugin: A convenience Factory for creating statistics.
SequenceViewerExtension.StatisticsFactory() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsFactory
SequenceViewerExtension.StatisticsSection - Class in com.biomatters.geneious.publicapi.plugin: One or more lines of statistics that show up in the statistics section of the sequence viewer.
SequenceViewerExtension.StatisticsSection(String, Number, String, double) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection: Creates a new statistics section
serviceAdded(WritableDatabaseService) - Method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities.WritableDatabaseServicesListener: Called by Geneious when a new service has been added.
serviceRemoved(WritableDatabaseService) - Method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities.WritableDatabaseServicesListener: Called by Geneious when a service has been removed.
serviceTreeLabelChanged() - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousServiceListener: Called when service tree label (GeneiousService.getName()) has changed.
ServiceUtilities - Class in com.biomatters.geneious.publicapi.plugin: Provides various utility functionality dealing with GeneiousServices.
set(int, T) - Method in class com.biomatters.geneious.publicapi.utilities.ConcatenatedList
set(int, int) - Method in class com.biomatters.geneious.publicapi.utilities.IntList.Array: sets the value of the list at the given index
setAcceptsUnknownPossibleValues(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption: Sets whether or not this combo box allows Options.Option.setValue(Object) or Options.setStringValue(String, String) to accept values not in the list of ComboBoxOrRadioOption#getPossibleOptionValues().
setAction(Action) - Method in class com.biomatters.geneious.publicapi.components.MoreOptionsButton
setAction(Action) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Button
setAction(Action) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBoxMenuItem
setAction(Action) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.MenuItem
setAction(Action) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ToggleButton
setAdditionalXml(String, boolean, Element) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Stores additional data in the form of XML which is directly associated with this document.
setAdditionalXml(Map<String, ElementProvider>, boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Stores additional data in the form of XML which is directly associated with this document.
setAdvanced(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Set this option as an advanced option, which means it will only appear in the advanced options panel.
setAdvancedOptionsInitiallyVisible(boolean) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Set whether the advanced options panel or message is visible initially if a 'More Options Dialog' is shown with these options.
setAlignmentDataForSequencesNotInMemory(SequenceListOnDisk.AlignmentData) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Replaces or sets all sequences (and associated data) in this alignment that are not the reference sequence (if any - see DefaultAlignmentDocument.getContigReferenceSequenceIndex().
setAlignmentOptions(String) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
setAllDocumentsUsedWhenNothingSelected(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption: Set whether all documents of the given type are used when nothing is selected.
setAllOutputDocumentsActive(boolean) - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument: Equivalent to calling OperationRecordDocument.setOutputDocumentActive(URN, boolean) on each document returned from OperationRecordDocument.getOutputDocuments()
setAllowAsOwnerOfOtherDialogs(boolean) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Normally a dialog will not be used as the owner of other dialogs (unless explicitly specified as the owner).
setAllowChangingFolderProperties(boolean) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Prevent this folder from being moved, renamed or removed.
setAllowDuplicateReferenceSequenceNames(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput: Sets whether AssemblerInput.getReferenceSequence(int, jebl.util.ProgressListener) throws a DocumentOperationException if there are duplicate reference sequence names
setAllowMultipleSelection(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption: Sets whether or not selecting multiple files is allowed by this file selection option.
setAllowReverseComplement(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Set whether or not intervals in the reverse direction should be reverse complemented.
setAlwaysUsesDefaultPreferenceLocation(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Occasionally when dealing with Options we want some values to remain persistent across different sets of preferences.
setAnnotationColoringQualifier(String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Sets the name of a qualifier on each annotation in this track whose numeric value is used for determining the intensity of the color of that annotation is rendered in.
setAnnotationColoringQualifierColors(Map<Double, Color>) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Sets the color gradient for use with SequenceTrack.setAnnotationColoringQualifier(String).
setAnnotations(int, List<SequenceAnnotation>, boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Updates just the annotations on a sequence.
setAnnotations(List<SequenceAnnotation>) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocumentWithEditableAnnotations: Sets new annotations on this document, replacing the existing ones.
setAnnotations(int, List<SequenceAnnotation>, boolean) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
setAnnotations(List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
setAnnotations(int, List<SequenceAnnotation>, boolean) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
setAnnotations(List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
setAnnotations(List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument
setAnnotations(List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: See SequenceDocumentWithEditableAnnotations.setAnnotations(java.util.List)
setAnnotations(List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Sets the annotations stored in this track
setAnnotationsOnConsensus(List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Sets the annotations on the consensus sequence that will be returned from a later call to SequenceAlignmentDocument.getAnnotationsOnConsensus().
setAnnotationsOnConsensus(List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
setAnnotationsOnConsensus(List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
setAnyReferenceSequenceFromAnUndissolvedContig(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Sets if there are any reference sequences which are from an undissolved contig.
setAutoHideLabels(boolean) - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: If set to true and the toolbar is showing small icons, when the toolbar becomes too small to fit all of its buttons, labels on the buttons will be hidden automatically.
setAutoMinimize(int) - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame: Deprecated.
this isn't nice for the users. Don't use it.
setAvailableToWorkflows(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Sets whether or not a DocumentOperation or AnnotationGenerator is available to workflows.
setBaseElement(Element) - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: Set document base element.
setCache(DefaultSequenceDocument.Cache) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Sets the cache used for caching the vaules returned from DefaultSequenceDocument.getCharSequence() and DefaultSequenceDocument.getSequenceAnnotations().
setCancelable(boolean) - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame: Set whether this progress frame should be cancelable by the user.
setCancelButton(String) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Set the button which is treated as a cancel button.
setCancelButton(Dialogs.DialogAction) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Set the button which is treated as a cancel button.
setCancelButtonLabel(String) - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame: Set the label for the "Cancel" button.
setCenterText(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption: Whether to draw the label text centered
setCharactersAndBitsPerCharStatic(SequenceCharacterSets.CharacterSet, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
setChildOptionsCollapsed(String, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Set the collapsed state of child options added previously using Options.addCollapsibleChildOptions(String, String, String, Options, boolean, boolean).
setChromatogramPositionsForResidues(int[]) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
setChromatogramValues(int[][]) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
setCircular(boolean) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument: Set whether or not this sequence is circular.
setCircular(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
setCircular(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Set whether this sequence is circular.
setCircular(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
setCircularAlignmentLength(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Sets the alignment being built as circular as specified by SequenceAlignmentDocument.getCircularLength()
setCircularLength(int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Sets the circular length of this alignment.
setCloseAction(Dialogs.DialogAction) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Sets the action associated with clicking the windows's close button (the X in the top-right hand corner of the window in Windows).
setColor(Color) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Sets the text/icon color for this folder
setColor(Color) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics.setColor(java.awt.Color)
setCompactNamePatternStatic(Object) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
setComplete() - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame: Sets the progress to 100%, causing the frame to close if it is visible.
setComponentLocation(SequenceViewerExtension.ComponentLocation) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension: Sets the current location for this component.
setComponentPosition(int) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Set where the components (or right component in the case of OptionsPanel.addTwoComponents(javax.swing.JComponent, javax.swing.JComponent, boolean, boolean) are positioned (normally EAST, WEST or CENTER).
setComposite(Composite) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D
setConstraints(List<Constraint>) - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Set constraints on the value that can be given to this field.
setConstructorAccessorStatic(ConstructorAccessor) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
setContig(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Set if this is a contig.
setContigReferenceSequenceIndex(int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Set the index (if any) of the reference sequence in a contig.
setCopyOnWrite() - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Flags this PairedReadManager to be duplicated when it is modified to using one of the methods PairedReadManager.setMates(int, int, int, boolean) , PairedReadManager.removeSequence(int), PairedReadManager.addSequence(), PairedReadManager.reorderSequences(int[]).
setCreated(Date) - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: Set document date of creation.
setCreationDate(Date) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
setCurrentColorScheme(Color[], Color[]) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Sets the current color scheme used by the sequence viewer.
setCurrentModalDialog(Dialog) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: This method can be called just before displaying a modal dialog to let Geneious know that it should avoid popping up other windows such as progress frames while it is visible.
setCurrentValue(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousCheckBoxPreference: Deprecated.

This change will be reflected in the preference dialog of the program.
setCurrentValue(Object) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousComboBoxPreference: Deprecated.

This change will be reflected in the preference dialog of the program.
setCurrentValue(String) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousRadioButtonPreference: Deprecated.

This change will be reflected in the preference dialog of the program.
setCurrentValue(String) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousStringPreference: Deprecated.

This change will be reflected in the preference dialog of the program.
setCurrentValuesAsDefaults() - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions: Sets the current values of these multiple options as the default values.
setCustomIcon(Icon) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Set a custom icon to use instead of the standard JOptionPane ones.
setDatabase(DatabaseService) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Set the database folder that this document was generated from.
setDecimalPlacesDisplayed(int) - Method in class com.biomatters.geneious.publicapi.implementations.EValue: Set number of decimal places in representation.
setDecimalPlacesDisplayed(int) - Method in class com.biomatters.geneious.publicapi.implementations.Percentage: Set number of decimal places in representation.
setDefaultButton(String) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Set the button which is the dialogs default button.
setDefaultButton(Dialogs.DialogAction) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Set the button which is the dialogs default button.
setDefaultDialogOwner(Window) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: FOR INTERNAL USE ONLY, PLUGINS SHOULD NOT CALL THIS METHOD.
setDefaultValue(ValueType) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Changes the default value for this option.
setDefaultValues(String, Date, String) - Method in class com.biomatters.geneious.publicapi.implementations.structure.DefaultMolecularStructureDocument: Save internally name, creation date and contents.
setDefaultValues(String, Date, String) - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument: Set document fields and info from data.
setDefaultVisibleInTable(boolean) - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType: Set whether the fields of this note type are visible in the document table by default
setDependentPosition(Options.RadioOption.DependentPosition) - Method in class com.biomatters.geneious.publicapi.plugin.Options.RadioOption: Set the position of all options that are dependent (set with addDependent) on this RadioOpion.
setDescription(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.ExtendedSearchOption: Sets the description of this option to be displayed as a tooltip.
setDescription(String) - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Setter for the document field's description property.
setDescription(String) - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType
setDescription(String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Sets the description of this sequence.
setDescription(String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: Set the human-readable graph description.
setDescription(String) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Set the description of the action.
setDescription(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Set a one line description for this option.
setDisabledValue(ValueType) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Changes the value observed through Options.Option.getValue() when the option is disabled (i.e.
setDocument(Document) - Method in class com.biomatters.geneious.publicapi.components.GTextField
setDocumentVisibleByDefaultOn(URN) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Sets the document that this track is only visible by default on.
setDoRevisionNumberChecks(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments: When SequenceSelectionWithDocuments.getSequences() is called, checks are made to make sure that the revision of the document hasn't changed and will throw a SequenceSelectionWithDocuments.SelectedDocumentsModifiedException if so.
setDoubleOnly() - Method in class com.biomatters.geneious.publicapi.components.GTextField: Set this component to only accept Double formatted values
setEditable(boolean) - Method in class com.biomatters.geneious.publicapi.components.GComboBox
setEditable(boolean) - Method in class com.biomatters.geneious.publicapi.components.GTextArea
setEditable(boolean) - Method in class com.biomatters.geneious.publicapi.components.GTextPane
setEditingEnabled(boolean, String) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer: This method should be overridden if the viewer allows editing of documents.
setEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogAction: Sets the enabled state of the DialogAction.
setEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Button
setEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBox
setEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBoxMenuItem
setEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ComboBox
setEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Label
setEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Menu
setEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.MenuItem
setEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ToggleButton
setEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
setEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions: Sets the enabled state of all these MultipleOptions.
setEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Set whether this option is currently enabled
setEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.OptionValue: Sets whether or not this option value is enabled.
setEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Sets the enabled state of all these Options.
setEnumerationValues(String[]) - Method in class com.biomatters.geneious.publicapi.documents.DocumentField: Sets the enumeration values.
setEnumerationValues(String[]) - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Set the list of values that this field may take.
setExecutableFlags(File) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Set the executable flag on a file, or do nothing if the OS does not support this behaviour Since Geneious 5.1.2 will accept a directory as argument to world execute on the entire directory tree
setExtraPersistentInformation(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.EditableComboBoxOption
setExtraPersistentInformation(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption
setExtraPersistentInformation(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Sets any information in addition to the option value that should be persistent between instances.
setField(DocumentNoteField) - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType: Add or modify a field.
setFieldValue(String, Object) - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: Set value of one data item (field).
It is important to call AbstractPluginDocument.addDisplayableField(DocumentField) if this field should be displayable and isn't already on this document. For non displayable fields, the value must either implement XMLSerializable or be an instance of a simple type that Geneious knows how to serialize (e.g.
setFieldValue(DocumentField, Object) - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: Set value of one data item (field).
setFieldValue(DocumentField, Object) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Set the value of field which is visible in the user interface.
setFieldValue(String, Object) - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNote: Set a value for a particular field.
setFieldValue(int, DocumentField, Object, boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Sets the value of a displayable field on one of the sequences in the alignment.
setFieldValue(int, DocumentField, Object, boolean) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
setFieldValue(String, Object) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
setFieldValues(Map<String, Object>) - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: Set all fields in one go.
setFillHorizontalSpace(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Set whether this option's component should fill all available horizontal space.
setFinalStatus(String, boolean) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: Sets a final status to be displayed to the user in the status bar when the search is finished.
setFindAll(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Findable.FindOptions: Sets the search to do a "find all" (i.e.
setFinishedAddingOutputDocuments() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument: tells this Operation Record that we're done adding documents via OperationRecordDocument.addOutputDocument(URN).
setFirstName(String) - Method in class com.biomatters.geneious.publicapi.documents.Author: Sets the first name of the author.
setFixedWidthFont(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleLineStringOption: Set whether the font in the text area should be fixed width
setFocusComponent(JComponent) - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: set an optional component to be focused when any of the actions are invoked or null to have no component focused.
setFolderViewDocument(AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: Instead of calling RetrieveCallback.setPropertyFields(java.util.List, com.biomatters.geneious.publicapi.documents.DocumentField) this method may be called to provide a document that may be used to provide a document style view on the entire results of the search.
setFolderViewDocument(AnnotatedPluginDocument, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Sets the folder view document on this folder.
setFont(Font) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics.setFont(java.awt.Font)
setFreeEndGapAlignment(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Set whether or not this alignment is considered to have free end gaps.
setGenerateContigs(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput: Sets whether or not contigs should be saved by the assembly.
setHasEndGapsStatic(boolean, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
setHasTrimsStatic(boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
setHidden() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Marks this option as a hidden option, i.e.
setHiddenFieldValue(DocumentField, Object) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Set the value of field which is not visible in the user interface.
setHorizontallyCompact(boolean) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Set whether this panel should layout its componets in a visually compact form suitable for displaying in a limited amount of space.
setHorizontallyCompact(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Flags the basic options to be displayed in a visually compact form suitable for displaying in a limited amount of space.
setHorizontallyCompactAdvanced(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Flags the advanced options to be displayed in a visually compact form suitable for displaying in a limited amount of space.
setIcon(Icon) - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption: Sets an icon that will be displayed to the left of the label.
setIcons(Icons) - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame: Set the icons for the frame/task bar (displayed in the left corner of the title bar).
setIcons(Icons) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Set the icons of the action.
setIcons(Icons) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Sets Icons associated with these options.
setIconSizeOptionEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: Set whether the icon size option is available in the popup menu.
setIncludeIntersectingAnnotations(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Sets whether or not the result returned from the extraction should include annotations which intersect the extracted region rather than being contained within it entirely.
setInitials(String) - Method in class com.biomatters.geneious.publicapi.documents.Author: Sets the initials of the author.
setInMainToolbar(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Set the location of this actio in the main toolbar (with the default position of 0.5 - see GeneiousAction.setInMainToolbar(boolean, double)).
setInMainToolbar(boolean, double) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Set the location of this action in the main toolbar.
setInMainToolbar(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Set the location of these action options in the main toolbar (with the default position of 0.5 - see GeneiousActionOptions.setInMainToolbar(boolean, double)).
setInMainToolbar(boolean, double) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Set the location of these action options in the main toolbar.
setInPopupMenu(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Set the location of this action in the popup menu (with the default position of 0.5 - see GeneiousAction.setInPopupMenu(boolean, double)).
setInPopupMenu(boolean, double) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Set the location of this action in the popup menu.
setInPopupMenu(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Set the location of these action options in the popup menu (with the default position of 0.5 - see GeneiousActionOptions.setInPopupMenu(boolean, double)).
setInPopupMenu(boolean, double) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Set the location of these action options in the popup menu.
setInScrollPane(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Specifies whether the options should be displayed in a scroll pane if the panel is shrunk below it's preferred size.
setInsets(Insets) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel.RoundedLineBorder: Set the inserts to use.
setInSplitLayout(DocumentViewer.ViewerLocation) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer: This method can optionally be overridden so the viewer is notified when it becomes part of a split layout (multiple views on the same document).
setInt(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
setIntegerOnly() - Method in class com.biomatters.geneious.publicapi.components.GTextField: Set this component to only accept Integer formatted values
setInterlaced(int, PairedReadManager.Orientation) - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Marks all the reads in the data set as being interlaced with the given orientation.
setIntervals(List<SequenceAnnotationInterval>) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: set the intervals on this annotation
setIntervals(List<SequenceAnnotationInterval>) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Set the intervals to extract.
setLabelComponent(JLabel) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Sets the label component associated with this Option so that its visibility and enabled state change correctly when the associated Option changes visibility or enabled.
setLabelPosition(int) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Set where the labels (or left component in the case of OptionsPanel.addTwoComponents(javax.swing.JComponent, javax.swing.JComponent, boolean, boolean) are positioned (normally EAST, WEST or CENTER).
setLargeIconLabelHorizontal(boolean) - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: By default, the toolbar displays text beside the icon only if we are using small icons.
setLargeIcons(boolean) - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: Set whether to display large icons (24x24 pixels) or small icons (16x16 pixels) for all buttons.
setLengthOfReferenceSequences(long) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Deprecated.
use AssemblerInput.Properties.setLengthOfReferenceSequences(long, long) instead
setLengthOfReferenceSequences(long, long) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Sets the total length of all reference sequences or 0 if there are no reference sequences.
setLocationOptions(OperationLocationOptions) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperationInput: Sets the location options to be used for this operation.
setMainFrame(AbstractFrame) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: Set the main Geneious frame.
setMainMenuLocation(GeneiousActionOptions.MainMenu) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Set the location of this action in the main menu (with the default position of 0.5 - see GeneiousAction.setMainMenuLocation(com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions.MainMenu, double)).
setMainMenuLocation(GeneiousActionOptions.MainMenu, double) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Set the location of this action in the main menu.
setMainMenuLocation(GeneiousActionOptions.MainMenu) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Set the location of these action options in the main menu (with the default position of 0.5 - see GeneiousActionOptions.setMainMenuLocation(com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions.MainMenu, double)).
setMainMenuLocation(GeneiousActionOptions.MainMenu, double) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Set the location of these action options in the main menu.
setMarkUnselectedDocumentsUnread(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback: Sets whether or not documents added to the callback that can't be immediately selected are marked as unread.
setMatchRegions(String) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Sets information about the matching regions of a local alignment.
setMates(int, int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: Sets 2 sequences as mates with the given expected mate distance.
setMates(int, int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Records the 2nd sequence as being paired with the first sequence with the given distance.
setMates(int, int, int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Records the 2nd sequence as being paired with the first sequence with the given distance.
setMates(int, int, int) - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Records the 2nd sequence as being paired with the first sequence with the given distance.
setMaxHeight(int) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Set the maximum height that the dialog will pack itself to.
setMaximumNumberOfContigsToGenerate(int) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput: For performance reasons, the user may limit the algorithm to generating this many contigs.
setMaximumSequenceLength(long) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Sets the maximum length of all sequences, excluding any reference sequences
setMaximumZoomLevel(double) - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: Set the maxiumum (most zoomed in) zoom level
setMaxWidth(int) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Set the maximum width that the dialog will pack itself to.
setMessage(String) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousServiceListener: Set a message which will be display immediately in the status bar if the service is selected.
setMinimumAndFitToScreenZoomLevel(double) - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel
setMinimumAndMaximumAndCurrentZoomLevels(double, double, double, boolean) - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: Set the minimum, maximum and current zoom level.
setMinimumAndMaximumAndCurrentZoomLevels(double, double, double, double, boolean) - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: Set the minimum, maximum, fit to screen and current zoom level.
setMinimumSequenceLength(long) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Sets the minimum length of all sequences, excluding any reference sequences
setModal(boolean) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: Set whether the dialog should be modal.
setMoreOptions(boolean) - Method in class com.biomatters.geneious.publicapi.components.MoreOptionsButton: Set whether this button is in "More Options" or "Fewer Options" state.
setMoreOptionsButtonText(String, String) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions: If any of the showMoreOptionsDialog methods are used to show a dialog with these options then the specified text will be used on the More/Fewer Options button.
setMustGenerateDefaultSequenceDocument(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Sets whether or not the result returned from the extraction must be a DefaultSequenceDocument.
setMustGenerateLinearSequence(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Sets whether or not the result returned from the extraction must be a linear sequence, even if extracting the entire length of a circular sequence.
setName(String) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Set document name.
setName(String) - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Setter for the document field's name property.
setName(String) - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType
setName(String) - Method in interface com.biomatters.geneious.publicapi.documents.Renamable: Sets the name of this object
setName(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: Sets the name of this document.
setName(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
setName(String) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
setName(String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Change the name of the sequence.
setName(String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: Set the name of the graph.
setName(String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Changes the name of this track
setName(String) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Set the name of the action.
setNexusSource(String, int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument: Set source of document in nexus format.
setNote(DocumentNote) - Method in interface com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.DocumentNotes: Add a note to this document (if no note with the same code exists) or update a note (if a note with the same code does exist).
setNoteType(DocumentNoteType) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentNoteUtilities: Can be used to add a new DocumentNoteType to the program if this DocumentNoteType does not already exist.
setNotRunningTest() - Static method in class com.biomatters.geneious.publicapi.plugin.TestGeneious: This is the first thing called by the application main() method.
setNumberOfBitsUsedToStoreLengthStatic(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
setNumberOfColumns(int) - Method in class com.biomatters.geneious.publicapi.plugin.Options.StringOption: Sets the number of columns used for displaying the value of this option.
setNumberOfIntegersOfStorage(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
setNumberOfMappedLocationsBitsStatic(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
setNumberOfNucleotidesInAllSequences(long) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Sets the number of bases in total in all the input sequences, excluding any reference sequences
setNumberOfPairedSequences(long) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Sets the number of sequences which are paired with another sequence.
setNumberOfReferenceSequences(long) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Sets the number of reference sequences.
setNumberOfSequences(long) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Sets numberOfSequences the number of sequences in the data, excluding any reference sequences
setNumberOfSequencesWithQuality(long) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Sets the number of sequences (excluding any reference sequences) which have quality (i.e.
setOpaque(boolean) - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar
setOptionsForActivelyLinkedDescendants(Element, List<AnnotatedPluginDocument>, List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback: This method will only have an effect if DocumentOperation.OperationCallback.isInterestedInParentDescendants() returns true.
setOptionsForActivelyLinkedDescendants(Element, List<AnnotatedPluginDocument>, List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback.Wrapper
setOriginalResidueNumbering(EditableSequenceDocument, int, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: set the original residue numbering of a document the residue index of a document will appear shifted if the user has "show original residue numbers" selected in the sequence view
setOutgoingMessageHandler(DocumentViewerMessageHandler) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewer: Set the outgoing message handler.
setOutputDocumentActive(URN, boolean) - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument: Sets whether or not the output document with this URN is active.
setOverrideName(String) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Sets the name of the extracted sequence.
setOverrideShortcut(KeyStroke) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Set a shortcut keystroke to override the default.
setPaint(Paint) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics2D.setPaint(java.awt.Paint)
setPaintBorderOnlyOnMouseOver(boolean) - Method in class com.biomatters.geneious.publicapi.components.GButton: Sets whether or not this buttons border is only painted when the mouse is over the button
setPairedReadsManager(PairedReadManager) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument: Sets a paired read manager to correspond with the nucleotide sequences for this document.
setParentOperationRecord(URN) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Sets a record of the operation that generated this document.
setPopupEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: Set whether the user should be able to right-click on the toolbar to change its properties via a popup menu.
setPopupIcons(Icons) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction.SubMenu: Set the icons which should be used for this action when it is displayed as a toolbar button.
setPositiveIntegerOnly() - Method in class com.biomatters.geneious.publicapi.components.GTextField: Set this component to only accept positive Integer formatted values
setPossibleValues(List<? extends ValueType>) - Method in class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption: Set the values the user can select from in the combo box.
setPotentialAnnotationsToExtract(Set<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Tells the extract code which annotations are allowed to end up on the extracted sequence.
setPreferredHeight(int) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Sets the preferred height of the component which will be returned from Options.Option.getComponent(), keeping the component at its current preferred width.
setPreferredWidth(int) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Sets the preferred width of the component which will be returned from Options.Option.getComponent(), keeping the component at its current preferred height.
setProgressListener(ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Sets a progress listener to report progress to during extraction and to allow a slow extraction call to be canceled.
setProOnly(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Set whether this action requires an active license.
setProOnly(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Set whether this action requires an active license.
setProOnly(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousPreference: Deprecated.
setProOnly(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Sets whether or not this option requires an active license.
setProOnly(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.OptionValue: Sets whether or not this option value requires an active license.
setProOnly(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Sets whether or not these options require an active license By default all options do not require an active license.
setProperties(AssemblerInput.Properties) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Assigns values to all properties by copying them from the given properties.
setProperty(String, String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: Sets a value on the internal properties object.
setPropertyFields(List<DocumentField>, DocumentField) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: Set query specific properties.
setPropertyRetrievalCallback(SequenceGraph.SequencePropertyRetriever) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Sets the SequencePropertyRetriever that will be returned from future calls to SequenceGraph.getSequencePropertyRetriever().
setQualifier(String, String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Deletes all existing qualifiers with the given name, and adds a new qualifier with the given value.
setQualifiers(List<SequenceAnnotationQualifier>) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Set a new list of qualifiers on this SequenceAnnotation, removing any existing qualifiers added via SequenceAnnotation.addQualifier(String, String) or SequenceAnnotation.addQualifier(SequenceAnnotationQualifier) or SequenceAnnotation.addQualifiers(java.util.Collection) or SequenceAnnotation.setQualifiers(java.util.List)
setQualifiers(List<SequenceAnnotationQualifier>) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Replaces all existing qualifiers on this track with a new list of qualifiers
setQueryCentricAlignment(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: Sets whether or not this alignment is a query centric alignment.
setReferencedAnnotatedDocuments(String, List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.documents.DocumentHistoryEntry: Have this entry reference some other annotatedPluginDocuments that are relevant to this entry in some way.
setReferencedDocument(int, AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Sets the sequence at the given sequenceIndexInAlignment in this alignment to refer to the given document as if it is the original source.
setReferencedDocument(int, AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
setReferencedDocument(int, AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
setReferencedSequence(int, SequenceAlignmentDocument.ReferencedSequence, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Sets the sequence at the given index in this alignment to refer to the given document as if it is the original source.
setReferencedSequence(int, SequenceAlignmentDocument.ReferencedSequence) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Equivalent to setReferencedSequence(sequenceIndexInAlignment, referencedSequence, -1
setReferencedSequence(int, SequenceAlignmentDocument.ReferencedSequence, int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
setReferencedSequence(int, SequenceAlignmentDocument.ReferencedSequence) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
setReferencedSequenceListDocument(int, AnnotatedPluginDocument, int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
setReferenceSequences(List<AssemblerInput.ReferenceSequence>) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Sets reference sequences currently selected by the user in the options.
setRemoteJobId(GeneiousService, String) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback: This method is only provided for core Geneious use when implementing a remote service such as a Geneious Server or a Green Button service.
setRemoteJobId(GeneiousService, String) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback.Wrapper
setRemoveGaps(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Set whether or not gaps should be removed during extraction.
setRenderingHint(RenderingHints.Key, Object) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics2D.setRenderingHint(java.awt.RenderingHints.Key, Object).
setResidues(List<CharSequence>, List<NucleotideGraph>, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Sets the residues of the sequence or alignment document that the graph applies to.
setResiduesOnly(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Set whether or not to ignore any annotations on the source sequence, and extract the residues only.
setRestoreDefaultApplies(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Set whether calling Options.restoreDefaults() should restore this setting to its default value.
setRestorePreferenceApplies(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Set whether calling Options.restorePreferences() should restore this setting to its value saved in preferences.
setResultsLocation(WritableDatabaseService) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperationInput: Sets the results location to be used for this operation.
setResumableState(Element) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback: Sets a resumable state for your operation.
setResumableState(Element) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback.Wrapper
setReturnElementsTwice() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ExternalSort: Flags this sorter to return all the elements twice.
setReverseSort(boolean) - Method in class com.biomatters.geneious.publicapi.documents.DocumentField: DocumentField.reverseSort
setRunningApplication() - Static method in class com.biomatters.geneious.publicapi.plugin.TestGeneious: This is second thing (after TestGeneious.setNotRunningTest() when starting the Geneious application.
setSavePreferencesForInvisibleChildOptions(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Sets whether or not calling restore defaults (Options.restoreDefaults()) or save preferences (Options.savePreferences()) will apply only to the child options (ChildOptions that are currently visible.
setSaveUnusedReads(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput: Sets whether or not unused reads should be saved by the assembly.
setSaveUsedReads(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput: Sets whether or not used reads should be saved by the assembly.
setSaveUsedReadsIncludeMates(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput: Sets whether or not the mates of used reads (even if that mate doesn't map) should be saved by the assembly.
setScore(Double) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument: set the score of this alignment, or null if no score was calculated.
setSearchResumptionIdentifier(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: Deprecated.
Geneious no longer supports resuming searches
setSelectable(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption: Sets whether or not the text in this label is selectable by the user.
setSelectableValues(String[]) - Method in class com.biomatters.geneious.publicapi.plugin.Options.EditableComboBoxOption: Replace the selectable values that this Option has.
setSelected(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction.ToggleAction: Set the selected state of the action
setSelectedAnnotations(List<SequenceViewerExtension.SequenceAnnotationWrapper>) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor: Sets the selected annotations
This method may only be invoked from the Swing thread
setSelectedIndex(int) - Method in class com.biomatters.geneious.publicapi.components.GComboBox
setSelectionType(int) - Method in class com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption: Set whether files and/or folders can be selected when browsing.
setSequenceAndAnnotations(CharSequence, List<SequenceAnnotation>) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.EditableSequenceDocument: Sets the sequence and annotations of this document.
setSequenceAndAnnotations(CharSequence, List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
setSequenceAndAnnotations(CharSequence, List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
setSequenceAndAnnotations(CharSequence, List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
setSequenceAndAnnotations(CharSequence, List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument
setSequenceAndAnnotations(CharSequence, List<SequenceAnnotation>) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: Equivalent to EditableSequenceDocument.setSequenceAndAnnotations(CharSequence,java.util.List).
setSequenceAndAnnotationsAndGraph(CharSequence, List<SequenceAnnotation>, NucleotideGraph) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.EditableNucleotideGraphSequenceDocument: Replaces EditableSequenceDocument.setSequenceAndAnnotations(CharSequence,java.util.List) which you must not call on a NucleotideGraphSequenceDocument.
setSequenceAndAnnotationsAndGraph(CharSequence, List<SequenceAnnotation>, NucleotideGraph) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideGraphSequenceDocument
setSequenceAndAnnotationsAndGraph(CharSequence, List<SequenceAnnotation>, NucleotideGraph) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
setSequenceAndAnnotationsAndGraph(CharSequence, List<SequenceAnnotation>, NucleotideGraph) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: Same as EditableNucleotideGraphSequenceDocument.setSequenceAndAnnotationsAndGraph(CharSequence, java.util.List, com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph) except that sequence may be null.
setSequenceName(int, String, boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: change the name of a sequence within the alignment.
setSequenceName(int, String, boolean) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
setSequenceName(int, String, boolean) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
setSequenceName(int, String, boolean) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
setSequenceQualities(int[]) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
setSequenceSelection(SequenceSelection) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperationInput: Sets the sequence selection to be used for this operation.
setSequenceSelection(SequenceSelection, String) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentViewerMessageHandler: Notifies when the selected sequence or residues has changed in a viewer.
setShortcutKey(KeyStroke) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction: Set the shortcutKey for this action (eg.
setShortcutKey(KeyStroke) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Set the shortcutKey for the action (eg.
setShouldSaveValue(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Sets whether the option will not save its value to preferences and save its value when you call Options.valuesToXML(String) on its parent options.
setShowLabels(boolean) - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar: Set whether or not text labels are showing on all buttons.
setSingleContigMappingToReferenceSequenceFromSeparateDocument(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Sets the result of AssemblerInput.Properties.isSingleContigMappingToReferenceSequenceFromSeparateDocument()
setSingleInputContig(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties: Sets if there is just a single contig being provided as input to the assembler.
setSmall(boolean) - Method in class com.biomatters.geneious.publicapi.components.GButton: Set whether this label should use a smaller font.
setSmall(boolean) - Method in class com.biomatters.geneious.publicapi.components.GComboBox: Set whether this GComboBox should use a smaller than normal font.
setSmall(boolean) - Method in class com.biomatters.geneious.publicapi.components.GLabel: Set whether this label should use a smaller font.
setSource(String, String, int) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument: Save original text used when tree was imported.
setSource(String, String) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument: Deprecated.
Geneious tree documents no longer store the original source, so this method does nothing.
setSourceService(DatabaseService) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Add an annotation to the document which tells the program which service to download the full document from if the PluginDocument is a summary (implements SummaryDocument)
AnnotatedPluginDocument.save() must be called afterwards to save the changes to the database.
setSpanningComponent(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Set whether the default generated panel treats this options's component as spanning when it has an empty label.
setStatus(String, long, boolean, long, long, long) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: Report download progress back to Geneious.
setStringValue(String, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: set the value of an option
setStroke(Stroke) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousGraphics2D: See Graphics2D.setStroke(java.awt.Stroke)
setStyleSheet(StyleSheet) - Method in class com.biomatters.geneious.publicapi.components.GTextPane.MemoryFixedHTMLEditorKit
setSubFolder(String) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback: Specify the name of a subfolder that the results of the operation should go in.
setSubFolder(String) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback.Wrapper
setSubMenuActions(List<GeneiousAction>) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction.SubMenu: Set the list of actions which will appear in the submenu/popup-menu.
setSummary(String) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Deprecated.
use setFieldValue(DocumentField.DESCRIPTION_FIELD, description) instead
setSuppressFailureOnClose(boolean) - Method in class com.biomatters.geneious.publicapi.utilities.ProgressInputStream: Sets suppressions of IOExceptions that occur when closing an InputStream.
setSurname(String) - Method in class com.biomatters.geneious.publicapi.documents.Author: Sets the surname of the author.
setTargetZoomLevel(double) - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: Sets the zoom level which is used for calculating the next zoom level from when pressing the 'zoom in' or 'zoom out' buttons.
setTemporaryFieldValue(String, Object) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: This us used for storing temporary in memory only information about this document.
setText(String, String) - Method in class com.biomatters.geneious.publicapi.components.MoreOptionsButton: Set the "More Options" and "Fewer Options" text.
setText(String) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Button
setText(String) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBox
setText(String) - Method in class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ToggleButton
setThresholdToStartThreads(int) - Method in class com.biomatters.geneious.publicapi.utilities.MultiThreadedProcessingSystem: Sets a threshold for the number of items to be added before this processing systems starts creating additional threads.
setTitle(String) - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame
setTitle(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback
setToolbarName(String) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Set name to be used when this action is displayed in the main toolbar.
setToolbarPosition(double) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions: Sets the relative position of these action options when they appear in a toolbar.
setTooltip(String) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogAction: Set a tooltip for the button associated with this action
setTrackColoringQualifiers(List<String>) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Store on this track a list of qualifiers that this track would like the Sequence Viewer to display as Track Colors.
setTranslation(GeneticCode, int) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Deprecated.
use SequenceExtractionUtilities.ExtractionOptions.setTranslation(GeneticCode geneticCode, int translationFrame, boolean removeFinalStopCodon, boolean translateFirstCodonUsingFirstCodonTable) instead.
setTranslation(GeneticCode, int, boolean, boolean) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Sets the extraction to translate while extracting.
setTrees(List<? extends Tree>) - Method in interface com.biomatters.geneious.publicapi.documents.types.EditableSameTaxaTreesDocument: Set some trees.
setTrees(List<? extends Tree>) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
setTrees(List<? extends Tree>) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
setTrees(List<? extends Tree>) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
setTruncateAnnotationsIfNecessary(boolean) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions: Sets whether or not to truncate annotations extending outside the extracted region so that they lie entirely within the extracted region.
setType(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Set the type of this annotation.
setUnread(boolean) - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Set read/unread (false/true) status.
setURN(URN) - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument: Set document URN.
setUserModificationAllowed(boolean) - Method in class com.biomatters.geneious.publicapi.documents.DocumentNoteField: Sets whether users are allowed to modify or remove this field.
setValue(Double) - Method in class com.biomatters.geneious.publicapi.implementations.Percentage: Change the current value of this percentage
setValue(String, String) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousPreferences: Deprecated.

Called for each GeneiousPreferences.GeneiousPreference, excluding GeneiousPreferences.GeneiousCheckBoxPreference, in these preferences when the user confirms by clicking OK and each time the program is started up (before initialisation).
setValue(String, boolean) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousPreferences: Deprecated.

Called for each GeneiousPreferences.GeneiousCheckBoxPreference in these preferences when the user confirms by clicking OK and each time the program is started up (before initialisation).
setValue(ValueType) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: set the current value of this option
setValue(ValueType, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: set the current value of this option
setValue(String, Object) - Method in class com.biomatters.geneious.publicapi.plugin.Options: set the value of an option
setValueFromString(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Set the value of this option from a string representation of the value
setValueOnComponent(JPanel, DocumentSelectionOption.FolderOrDocuments) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption
setValueOnComponent(JCheckBox, Boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.BooleanOption
setValueOnComponent(JPanel, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption
setValueOnComponent(JComboBox, Options.OptionValue) - Method in class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption
setValueOnComponent(JComponent, Date) - Method in class com.biomatters.geneious.publicapi.plugin.Options.DateOption
setValueOnComponent(GComboBox, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.EditableComboBoxOption
setValueOnComponent(Options.ExecutableFilePanel, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.ExecutableFileSelectionOption
setValueOnComponent(Options.FileSelectionPanel, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption
setValueOnComponent(JLabel, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption
setValueOnComponent(JScrollPane, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleLineStringOption
setValueOnComponent(ComponentType, ValueType) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Set the value on this component.
setValueOnComponent(JPanel, Options.OptionValue) - Method in class com.biomatters.geneious.publicapi.plugin.Options.RadioOption
setValueOnComponent(JTextField, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.StringOption
setValueOnComponent(JButton, Interval) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionGrabOption
setVerticallyCompact(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Flags the basic options to be displayed in a visually compact form suitable for displaying in a limited amount of space.
setVerticallyCompactAdvanced(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Flags the advanced options to be displayed in a visually compact form suitable for displaying in a limited amount of space.
setVerticalSpacing(int) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Deprecated.
use OptionsPanel.setVerticalSpacing(int, int) instead
setVerticalSpacing(int, int) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Sets the spacing above and below added componenents.
setVerticalWeight(double) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Set the weighting used to decide how much this component should stretch when its container is resized.
setVisible(boolean) - Method in class com.biomatters.geneious.publicapi.components.BubbleToolTip: Shows or hides the tooltip.
setVisible(boolean) - Method in class com.biomatters.geneious.publicapi.components.GPopupMenu
setVisible(boolean) - Method in interface com.biomatters.geneious.publicapi.documents.DocumentNoteType: Setting this to false will mean the user can not edit the note type at all and can not add new instances of the note type through the standard "Notes" user interface.
setVisible(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption
setVisible(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions: Sets the visibility of the graphical component that displays these multiple options and makes appropriate changes to the size of the window (if any) that contains the graphical component.
setVisible(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Sets the visibility of the graphical component that displays this option together with its label and makes appropriate changes to the size of the window (if any) that contains the graphical component.
setVisible(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Sets the visibility of the graphical component that displays these options and makes appropriate changes to the size of the window (if any) that contains the graphical component.
setVisibleOnlyWhenEnabled(boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption: If true, then calling Options.Option.setEnabled(boolean) will additionally have the effect of calling Options.LabelOption.setVisible(boolean)
setWarningMessage(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Sets a warning message displayed in a BubbleToolTip on the option component.
setWeightY(double) - Method in class com.biomatters.geneious.publicapi.components.OptionsPanel: Set the vertical weight of components added using methods that don't take weightY as a parameter.
setWorkingDirectory(String) - Method in class com.biomatters.geneious.publicapi.utilities.Execution: Set the working directory of the external process.
setWritingFinished() - Method in class com.biomatters.geneious.publicapi.utilities.Execution: Called when stdout has finished being read.
setZoomLevel(double) - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: Calls setZoomLevel(zoomLevel, true)
setZoomLevel(double, boolean) - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: Sets the zoom level.
SHIFT_KEY_STRING - Static variable in class com.biomatters.geneious.publicapi.utilities.GuiUtilities: System-dependent string used to represent the SHIFT key
shortcutChanged(String, KeyStroke) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions.ShortcutChangeListener: Called when the shortcut changes for a GeneiousActionOptions
shouldCreateContigOnDisk(int, int) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Returns true if the sequence count and/or reference length of this contig are sufficient for it to be recommended to create a contig on disk.
shouldSaveValue() - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption
shouldSaveValue() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: If this method returns false, then the option will not save its value to preferences, nor will it save its value when you call Options.valuesToXML(String) on its parent options.
show(Component, int, int) - Method in class com.biomatters.geneious.publicapi.components.GPopupMenu
showApplyToAllDialog(Dialogs.DialogOptions, String) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog with an "Apply to all" checkbox, which, if checked, signifies that the result from showing this dialog should be used in all cases
showComboBoxDialog(String, String[], String, String, Component) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show an OK/Cancel dialog to the user with a non-editable combo-box in it.
showContinueCancelDialog(String, String, Component, Dialogs.DialogIcon) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog to the user with "Continue" and "Cancel" buttons.
showDialog(Dialogs.DialogOptions, String) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog with a String message to the user with the specified dialog options.
showDialog(Dialogs.DialogOptions, Component) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog with a custom Component to the user with the specified dialog options.
showDialog(Dialogs.DialogOptions, String, JComponent) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog with a String message to the user with the specified dialog options.
showDialog(Dialogs.DialogOptions, Component, JComponent) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog with a custom component to the user with the specified dialog options.
showDialogWithDontShowAgain(Dialogs.DialogOptions, String, String, String) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Display a dialog to the user with something like a 'Don't show again' check box.
showDialogWithDontShowAgain(Dialogs.DialogOptions, Component, String, String) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Display a dialog to the user with something like a 'Don't show again' check box.
showDialogWithRememberMyPreference(Dialogs.DialogOptions, String, String, String) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog to the user with a 'Remember my preference' check box.
showInputDialog(String, String, Component, JComponent...) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show an OK/Cancel dialog to the user with custom input components.
showInServiceTree() - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService
showInServiceTree() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: Override and return false to hide this service from the service tree.
showMessageDialog(String, String, Component, Dialogs.DialogIcon) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog to the user with a string message and just an "OK" button.
showMessageDialog(String, String) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog to the user with a string message and just an "OK" button.
showMessageDialog(String) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog to the user with a string message and just an "OK" button.
showMoreOptionsDialog(Dialogs.DialogOptions, String, String) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog to the user with two string messages.
showMoreOptionsDialog(Dialogs.DialogOptions, Component, Component) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog to the user with two custom components.
showOkCancelDialog(String, String, Component) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog to the user with "OK" and "Cancel" buttons.
showOkCancelDialog(Component, String, Component) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog to the user with "OK" and "Cancel" buttons.
showOkCancelDialog(String, String, Component, Dialogs.DialogIcon) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog to the user with "OK" and "Cancel" buttons.
showOkCancelDialog(Component, String, Component, Dialogs.DialogIcon) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog to the user with "OK" and "Cancel" buttons.
showOkDialogWithDontShowAgain(Component, String, String, String) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Display a dialog to the user with only an OK button and a "Don't show this again" check box.
showOptionsDialog(Options, String, boolean) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Display an options dialog based on an Options object.
showOptionsDialog(Options, String, boolean, JComponent) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Display an options dialog based on an Options object.
showSaveAsDialog(JComponent) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Shows the "Save As" dialog (i.e.
showSaveChangesDialog(String, Component) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a save changes dialog that has options equivalent to the values in Dialogs.SaveChanges.
showSequenceView() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
showTextFieldDialog(String, String, String, Component) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show an OK/Cancel dialog to the user with a text field in it.
showYesNoDialog(String, String, Component, Dialogs.DialogIcon) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog to the user with "Yes" and "No" buttons.
showYesNoDialog(Component, String, Component, Dialogs.DialogIcon) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog to the user with "Yes" and "No" buttons.
showYesNoDialogWithRememberMyPreference(Component, String, String, String) - Static method in class com.biomatters.geneious.publicapi.components.Dialogs: Show a dialog to the user with Yes and No buttons and a "Remember my preference" check box.
shutdown() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: This method is called Geneious is shutting down or the plugin that provided this service is being disabled.
size() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResultsOnSingleSequence
size() - Method in class com.biomatters.geneious.publicapi.utilities.ConcatenatedList
size() - Method in class com.biomatters.geneious.publicapi.utilities.IntList.Array
size() - Method in class com.biomatters.geneious.publicapi.utilities.IntList: Returns the size of this list like List.size()
size() - Method in class com.biomatters.geneious.publicapi.utilities.WeakSimpleListenerManager
skip(long) - Method in class com.biomatters.geneious.publicapi.utilities.ProgressInputStream: Overrides FilterInputStream.skip to update the progress listener after the skip.
sleep(long) - Static method in class com.biomatters.geneious.publicapi.utilities.ThreadUtilities: A convenience method for calling Thread.sleep(long) without having to worry about handling the interrupted exception.
sort(List<T>) - Static method in class com.biomatters.geneious.publicapi.utilities.GeneralUtilities: Just like Collections.sort(java.util.List) but much faster in cases where list.size()<=2.
sort(List<T>, Comparator<? super T>) - Static method in class com.biomatters.geneious.publicapi.utilities.GeneralUtilities: Just like Collections.sort(java.util.List, java.util.Comparator) but much faster in cases where list.size()<=2.
sort(Object[]) - Static method in class com.biomatters.geneious.publicapi.utilities.GeneralUtilities: Just like Arrays.sort(Object[]) but much faster in cases where list.size()<=2.
sort(T[], Comparator<? super T>) - Static method in class com.biomatters.geneious.publicapi.utilities.GeneralUtilities: Just like Arrays.sort(Object[], java.util.Comparator) but much faster in cases where list.size()<=5.
sort() - Method in class com.biomatters.geneious.publicapi.utilities.IntList.Array: sorts the values in this list in increasing order
SOURCE_QUALIFIER_NAME - Static variable in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Deprecated.
from 7.0.0, this field is not added to new primer annotations
split(int) - Method in class com.biomatters.geneious.publicapi.utilities.Interval: Splits this interval into 2 intervals such that everything <x is in one part of the interval and everything >=x is in the other part.
split(int...) - Method in class com.biomatters.geneious.publicapi.utilities.Interval: Splits this interval into multiple intervals such that no splitPosition is contained within any of the intervals.
splitIntoLines(String) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Splits a String into the lines it consists of, with any of the standard newlines (\r, \n or \r\n) being accepted (as by a BufferedReader).
StandardIcons - Enum in com.biomatters.geneious.publicapi.utilities: The set of standard icons used in Geneious.
startElement(String, String, String, Attributes) - Method in class com.biomatters.geneious.publicapi.utilities.xml.FilteredSaxHandler
statusChanged(GeneiousService.ServiceStatus) - Method in interface com.biomatters.geneious.publicapi.plugin.GeneiousServiceListener: Called when service status changes (when service becomes unavailable/available/busy).
stderrWritten(String) - Method in class com.biomatters.geneious.publicapi.utilities.Execution.OutputListener: Called by the default implementation of Execution.OutputListener.stdoutWritten(char) when a complete line of text has been written to standard error by the external process.
stderrWritten(char) - Method in class com.biomatters.geneious.publicapi.utilities.Execution.OutputListener: Called by the Execution instances when single character line of text has been written to standard error by the external process.
stdoutWritten(String) - Method in class com.biomatters.geneious.publicapi.utilities.Execution.OutputListener: Called by the default implementation of Execution.OutputListener.stdoutWritten(char) when a complete line of text has been written to standard out by the external process.
stdoutWritten(char) - Method in class com.biomatters.geneious.publicapi.utilities.Execution.OutputListener: Called by the Execution instances when a single character of text has been written to standard out by the external process.
stopCreatingOperationRecords() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback: Stops any operation records from being created for subsequent documents added using addDocument.
stopCreatingOperationRecords() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback.Wrapper
stringListFromXml(Element) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Deserializes a list of String elements which were serialized using XMLSerializer.stringListToXml(String, java.util.List).
stringListToXml(String, List<String>) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Serializes a list of Strings which can be deserialized using XMLSerializer.stringListFromXml(org.jdom.Element) in any version of Geneious from 5.6 onwards.
stringToList(String) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Converts a String created using StringUtilities.listToString(java.util.List) back into a list of Strings.
StringUtilities - Class in com.biomatters.geneious.publicapi.utilities: Provides utility methods for creating and manipulating Strings.
stripHtmlTags(String, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Strips all html tags and their contents from the provided String
STRONG_REFERENCED_DOCUMENT_PREFIX - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: If a qualifier value starts with this prefix, and the remainder of the qualifier value is a URN.toString() of a document, then it is assumed to be a strong reference to that document.
STRUCTURE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup: A group of 3d structure annotations, including SequenceAnnotation.TYPE_HELIX, SequenceAnnotation.TYPE_STRAND, SequenceAnnotation.TYPE_COIL, SequenceAnnotation.TYPE_TURN.
subList(int, int) - Method in class com.biomatters.geneious.publicapi.utilities.IntList.Array
subList(int, int) - Method in class com.biomatters.geneious.publicapi.utilities.IntList: Creates a sub list
subSelection(int...) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments: Given a set of indices specifying some of this class's SequenceSelection's intervals, determines which AnnotatedPluginDocuments are referenced by those SelectionIntervals, and groups them together into a List.
subSequence(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ByteBackedCharSequence
subSequence(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
subSequence(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Constructs a subsequence of this sequence.
subSequence(CharSequence, int, int) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities: Creates a CharSequence that starts at index start and finishes at index end-1 such that the length of the CharSequence is start - end.
subString(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Returns the characters between the 2 given indices as a string
SummaryDocument - Interface in com.biomatters.geneious.publicapi.documents: Any summary document should "implement" this empty interface to enable special handling of summary documents inside Geneious.
supportsAddingDatabasesFromDocumentsOrFiles() - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService: Return true to have the program display options for choosing a file or using the selected documents to create a database.
supportsAlphabet(SequenceDocument.Alphabet) - Method in class com.biomatters.geneious.publicapi.plugin.AlignmentOperation
supportsCompression(CompressionUtilities.CompressionMethod) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter: Returns true if this DocumentFileImporter is able to handle a specified type of compression.
supportsInputContigs() - Method in class com.biomatters.geneious.publicapi.plugin.Assembler: true if this assembly algorithm can accept contigs (SequenceAlignmentDocuments as input along with sequences.
supportsModifyingDatabases(DatabaseService.SequenceSearchQueryType) - Method in class com.biomatters.geneious.publicapi.databaseservice.SequenceDatabaseSuperService: Override and return true to enable the user interface for adding and removing of sequence databases of particular types from this service.
supportsReferenceSequencesWithDuplicateNames() - Method in class com.biomatters.geneious.publicapi.plugin.Assembler
supportsRenderingLargeRegions() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: True if the graph supports rendering large regions at one time.
supportsSingleInputContig() - Method in class com.biomatters.geneious.publicapi.plugin.Assembler: true if this assembly can accept single contigs as input and do some sort of fine tuning to improve the contig.
supportsSlidingWindows() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceGraph: Determine if the "sliding window size" option should apply to this graph.
supportsVersionSerialization(XMLSerializable.OldVersionCompatible) - Static method in enum com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType: Returns true if the given instance correctly supports version serialization.
SystemUtilities - Class in com.biomatters.geneious.publicapi.utilities: Provides utility methods for interacting with the operating system.

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TAXONOMY_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Visible, editable field representing a sequence's taxonomy.
TAXONOMY_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: TaxonomyDocument document type
TaxonomyDocument - Interface in com.biomatters.geneious.publicapi.documents.types: A plugin document containing one TaxonomyDocument.Taxon, which holds information (rank, scientific name and alternative names) about one taxon in a taxonomy, and a reference to its parent taxon (if any).
TaxonomyDocument.Taxon - Class in com.biomatters.geneious.publicapi.documents.types: A taxon (element of a taxonomy) consisting of its scientific name (e.g.
TaxonomyDocument.Taxon(String, TaxonomyDocument.TaxonomicLevel, TaxonomyDocument.Taxon, List<String>) - Constructor for class com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument.Taxon: Construct a new Taxon.
TaxonomyDocument.TaxonomicLevel - Enum in com.biomatters.geneious.publicapi.documents.types: Represents a taxonomic level (AKA rank) that a Taxon can have in a Taxonomy, e.g.
TEMPORARY_FIELD_KEY_ANNOTATED_DOCUMENT_LOCATION - Static variable in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Used by databases with AnnotatedPluginDocument.setTemporaryFieldValue(String,Object) for providing the user with information about the location of the AnnotatedPluginDocument.
TEMPORARY_FIELD_KEY_PLUGIN_DOCUMENT_LOCATION - Static variable in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Used by databases with AnnotatedPluginDocument.setTemporaryFieldValue(String,Object) for providing the user with information about the location of the PluginDocument.
tentativeAutoDetect(File, String) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileImporter: Attempts to detect whether a file is of the right type for this importer, based purely on the first up to 512 (this number may change in the future) characters of the file.
TestGeneious - Class in com.biomatters.geneious.publicapi.plugin: Provides methods to facilitate writing test cases for Geneious plugins
text - Variable in class com.biomatters.geneious.publicapi.documents.AdditionalSearchContent.Result: Search-able text.
TEXT_SEARCH_TYPE - Static variable in class com.biomatters.geneious.publicapi.databaseservice.TextOrSimilaritySearchOption
TextFieldSearchOption - Class in com.biomatters.geneious.publicapi.databaseservice: An extended search option which is displayed as a Text Field.
TextFieldSearchOption(String, String, String, Class) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.TextFieldSearchOption: The default constructor.
textFromElement(Element) - Static method in class com.biomatters.geneious.publicapi.documents.AdditionalSearchContent.Utilities: Get all text in element as a searchable content.
textFromElement(Element, AdditionalSearchContent.Utilities.FilterElement) - Static method in class com.biomatters.geneious.publicapi.documents.AdditionalSearchContent.Utilities: Get searchable text from text in element while observing the filtering rules in
TextOrSimilaritySearchOption - Class in com.biomatters.geneious.publicapi.databaseservice: A specialized option for local search.
TextOrSimilaritySearchOption(String) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.TextOrSimilaritySearchOption: The default constructor.
ThreadUtilities - Class in com.biomatters.geneious.publicapi.utilities: Provides utility methods for managing threads.
throwCause() - Method in exception com.biomatters.geneious.publicapi.plugin.RuntimeDocumentOperationException: Rethrows the cause of this exception
TM_FIELD - Static variable in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument: Displayable field for the melting point of the oligo
to - Variable in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature.DocumentSelectionSignatureAtom: Repeated N (from <= N < to) times.
toAlignmentDocument(ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Creates an Alignment document from this builder.
toArrowString() - Method in enum com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval.Direction
toCompactString() - Method in class com.biomatters.geneious.publicapi.documents.Author: Returns the same value as toString().
toEndGapsManager(SequenceListOnDisk<? extends SequenceDocument>) - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager.Builder: Creates an EndGapsManager from this builder
TOGGLED_PROPERTY_NAME - Static variable in class com.biomatters.geneious.publicapi.plugin.GeneiousAction.ToggleAction: The name of the property for which a propertyChange event is fired when the action is toggled
toHTML() - Method in class com.biomatters.geneious.publicapi.documents.DocumentCollection
toHTML() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
toHTML() - Method in interface com.biomatters.geneious.publicapi.documents.PluginDocument: Provide a textual view of document.
toHTML() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
toHTML() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
toHTML() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument
toHTML() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
toHTML() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
toHTML() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
toHTML() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
toHTML() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
toHTML() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument
toHTML() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: This method is not implemented.
toHTML() - Method in class com.biomatters.geneious.publicapi.implementations.structure.DefaultMolecularStructureDocument
toHTML() - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument
toHTMLFragment(SequenceDocument, String) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities: Generate a HTML fragment that summarises a sequence, including the sequence string.
toIntArray() - Method in class com.biomatters.geneious.publicapi.utilities.IntList.Array
toIntArray(int, int) - Method in class com.biomatters.geneious.publicapi.utilities.IntList.Array: returns a copy of a sub-list of the elements in this list as an array
toList() - Method in class com.biomatters.geneious.publicapi.utilities.WeakReferenceList: Creates a list of all objects added to this class that are still strongly referenced.
toOutputStream(GeneiousObjectOutputStream) - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Serializes this PairedReadManager to an output stream so that it can be reconstructed later using PairedReadManager.PairedReadManager(com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectInputStream).
toOutputStream(Geneious.MajorVersion, GeneiousObjectOutputStream) - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Serializes this PairedReadManager to an output stream so that it can be reconstructed later using PairedReadManager.PairedReadManager(com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectInputStream).
toPairedReadManager() - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager.Builder: Creates a new PairedReadManager from this builder.
TOPOLOGY_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Visible, editable field representing the topology of a sequence - either "linear" or "circular" Always displayed for sequence document (handled by core).
toSequenceList(ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Creates a SequenceListOnDisk from this builder.
toSequenceListDocument(ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder: Creates a new SequenceListDocument from this builder.
toString() - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogAction
toString() - Method in class com.biomatters.geneious.publicapi.databaseservice.CheckboxSearchOption
toString() - Method in class com.biomatters.geneious.publicapi.databaseservice.ExtendedSearchOption: Displays a summary of the properties of this option.
toString() - Method in class com.biomatters.geneious.publicapi.documents.Author
toString() - Method in class com.biomatters.geneious.publicapi.documents.Constraint
toString() - Method in class com.biomatters.geneious.publicapi.documents.DocumentField
toString() - Method in class com.biomatters.geneious.publicapi.documents.DocumentFieldAndValue
toString() - Method in enum com.biomatters.geneious.publicapi.documents.DocumentNoteField.Types: Returns the name of this Types object.
toString() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ByteBackedCharSequence
toString() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument.ReferencedSequence
toString() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Returns a human readable string with information about this annotation; the exact format of the string is not guaranteed and should not be relied on, because it may change at any time.
toString() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup
toString() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval
toString(boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval
toString(boolean, boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval
toString() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Returns a human readable string with information about this qualifier; the exact format of the string is not guaranteed and should not be relied on, because it may change at any time.
toString() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence
toString() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution.ValueAndFrequency
toString() - Method in class com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument.Taxon: Convert this Taxon and all of its ancestors to a String (i.e.
toString() - Method in class com.biomatters.geneious.publicapi.documents.URN: Returns the full URN as a string.
toString() - Method in class com.biomatters.geneious.publicapi.implementations.EValue
toString() - Method in class com.biomatters.geneious.publicapi.implementations.Percentage
toString() - Method in enum com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument.OligoType
toString() - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument
toString() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Properties
toString() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature
toString() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentType
toString() - Method in enum com.biomatters.geneious.publicapi.plugin.Geneious.MajorVersion
toString() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousAction
toString() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService
toString() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option: Call Options.Option.getDescriptionAndState()
toString() - Method in class com.biomatters.geneious.publicapi.plugin.Options.OptionValue
toString() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Call Options.getDescriptionAndState()
toString() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment
toString() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange
toString() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
toString() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex
toString() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection
toString(CharSequence) - Static method in class com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities: Constructs a String holding the same sequence of characters as the specified charSequence, without calling CharSequence.toString().
toString() - Method in class com.biomatters.geneious.publicapi.utilities.Interval
toString() - Method in class com.biomatters.geneious.publicapi.utilities.IntList
toStrings() - Static method in enum com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument.OligoType
toSummaryDocument() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: Generates a new AnnotatedPluginDocument that is identical to this document, except that the internal PluginDocument to a lightweight AnySummaryDocument.
toXML() - Method in class com.biomatters.geneious.publicapi.databaseservice.FolderView
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.FolderView
toXML() - Method in class com.biomatters.geneious.publicapi.databaseservice.QueryField
toXML() - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument
toXML() - Method in class com.biomatters.geneious.publicapi.documents.Author
toXML() - Method in class com.biomatters.geneious.publicapi.documents.DocumentCollection
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.DocumentCollection
toXML() - Method in class com.biomatters.geneious.publicapi.documents.DocumentField
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.DocumentField
toXML() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
toXML(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout: Converts this layout to XML for use with AlignmentLayout.AlignmentLayout(org.jdom.Element)
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.AlignmentLayout
toXML() - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
toXML(ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
toXML(boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence
toXML(Geneious.MajorVersion, ProgressListener, boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence
toXML() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Serialization of annotation - to.
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence
toXML(boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Serializes this SequenceCharSequence to XML into an element named XMLSerializable.ROOT_ELEMENT_NAME.
toXML(Geneious.MajorVersion, ProgressListener, boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Serializes this SequenceCharSequence to XML into an element named XMLSerializable.ROOT_ELEMENT_NAME.
toXML() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Serializes this SequenceCharSequence to XML into an element named XMLSerializable.ROOT_ELEMENT_NAME.
toXML(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.AlignmentData: Converts this AlignmentData to XML for later use with AlignmentData#AlignmentData(org.jdom.Element)
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.AlignmentData
toXML(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk: Converts this list to XML for use with storing in a PluginDocument.
toXML(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.PairwiseSimilarity: Converts this to XML
toXML() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary
toXML() - Method in class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution
toXML(String) - Method in class com.biomatters.geneious.publicapi.documents.URN: Convert a URN into a XML element.
toXML(Geneious.MajorVersion, ProgressListener) - Method in interface com.biomatters.geneious.publicapi.documents.XMLSerializable.OldVersionCompatible: Serializes this class to XML format, potentially to a format readable by an earlier version of Geneious.
toXML() - Method in interface com.biomatters.geneious.publicapi.documents.XMLSerializable: Convert object to a JDOM element.
toXML(ProgressListener) - Method in interface com.biomatters.geneious.publicapi.documents.XMLSerializableWithProgress: Convert object to a JDOM element.
toXML() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
toXML(ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
toXML() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
toXML() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultSameTaxaTreesDocument
toXML() - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultTreeDocument
toXML() - Method in class com.biomatters.geneious.publicapi.implementations.EValue: eg.
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.EValue
toXml(String) - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager: Serializes this PairedReadManager to XML so that it can be reconstructed later using PairedReadManager.PairedReadManager(org.jdom.Element)
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.PairedReadManager
toXML() - Method in class com.biomatters.geneious.publicapi.implementations.Percentage
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.Percentage
toXML() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
toXML() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence
toXML() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
toXML() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument
toXML(String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage: Convert object to a JDOM Element with the given name as the name of the root element.
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
toXML() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequencePropertiesStorage
toXML() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Serializes this manager to XML, using PluginDocument.FILE_DATA_ATTRIBUTE_NAME where appropriate.
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Serializes this manager to XML, using PluginDocument.FILE_DATA_ATTRIBUTE_NAME where appropriate.
toXML(String) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack: Serializes this track to XML for use with SequenceTrack.SequenceTrack(org.jdom.Element).
toXML(String) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Serializes this gap information (excluding the char sequence) to XML which may use PluginDocument.FILE_DATA_ATTRIBUTE_NAME
toXML(Geneious.MajorVersion, String) - Method in class com.biomatters.geneious.publicapi.implementations.SequenceGapInformation: Serializes this gap information (excluding the char sequence) to XML which may use PluginDocument.FILE_DATA_ATTRIBUTE_NAME
toXML() - Method in class com.biomatters.geneious.publicapi.implementations.structure.PdbDocument
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.OperationLocationOptions
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.Options.BooleanOption
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.Options.EditableComboBoxOption
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.Options.ExecutableFileSelectionOption
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.Options.LabelOption
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleLineStringOption
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.Options.OptionValue
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.Options.RadioOption
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.Options.StringOption
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.Options
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectionInterval
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.ExtractionStrategy
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.ExtractionStrategy
toXML() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments
toXML() - Method in class com.biomatters.geneious.publicapi.utilities.Interval
toXML(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.utilities.Interval
toXml(Element, Iterable<Element>, int, ProgressListener, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.xml.PluginDocumentXmlCollection: Serializes these elements into a single parent element, potentially storing them in a file (using PluginDocument.FILE_DATA_ATTRIBUTE_NAME)
toXMLAsWeakReference(String) - Method in class com.biomatters.geneious.publicapi.documents.URN: Convert a URN into a XML element.
toXMLExcludingInternalPluginDocument() - Method in class com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument: converts this AnnotatedPluginDocument to a single XML element.
toXmlExcludingSequences(String) - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager: Converts this EndGapsManager to XML, excluding the associated sequences, which must be stored independently and provided again during serialization using EndGapsManager.EndGapsManager(org.jdom.Element, com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk)
toXmlExcludingSequences(Geneious.MajorVersion, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.EndGapsManager: Converts this EndGapsManager to XML, excluding the associated sequences, which must be stored independently and provided again during serialization using EndGapsManager.EndGapsManager(org.jdom.Element, com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk)
transformSequence(SequenceDocument) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument.Transformer: Transforms a sequence
translate(SequenceDocument, SequenceAnnotation) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities: Deprecated.
use SequenceExtractionUtilities.extractIntervals(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions) instead.
TRANSLATED_REGION_INTERVALS_NAME - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Name to use for a SequenceAnnotationQualifier to specify that the SequenceAnnotation represents a translation.
translateUrns(Element, Map<URN, URN>) - Static method in class com.biomatters.geneious.publicapi.documents.XMLSerializer: Translates all URNs (i.e.
TREE_BUILDER_METHOD_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The method/algorithm used to build a tree.
TREE_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType: TreeDocument document type
TreeDocument - Interface in com.biomatters.geneious.publicapi.documents.types: The common base for all documents that hold one or several trees.
TreeViewerExtension - Class in com.biomatters.geneious.publicapi.plugin: A tree viewer extension is used for creating a custom controls section in the tree viewer.
TreeViewerExtension() - Constructor for class com.biomatters.geneious.publicapi.plugin.TreeViewerExtension
TreeViewerExtension.Factory - Class in com.biomatters.geneious.publicapi.plugin: The factory class that plugins provide via GeneiousPlugin.getTreeViewerExtensionFactories() for creating TreeViewerExtensions
TreeViewerExtension.Factory() - Constructor for class com.biomatters.geneious.publicapi.plugin.TreeViewerExtension.Factory
TRIMMED_SEQUENCES_COUNT - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: The number of sequences in an alignment or set of sequences that have trim annotations or are ImmutableSequences with either ImmutableSequence.getLeadingTrimLength() or ImmutableSequence.getTrailingTrimLength() greater than 0.
TRIMMING_EXTRACTION_STRATEGY - Static variable in class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments: An ExtractionStrategy that does what DefaultExtractionStrategy does, but additionally performs trimming on the sequences, such that any leading or trailing trim annotations are respected and these portions of the sequence are left out of the extraction.
trimToLength(String, int, boolean) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities: Trims this string so that it is at most maximumLength characters long.
truncate(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval: Truncates this interval to not extend below minIndex or above maxIndex.
TYPE_CDS - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_CHAIN - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_COIL - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_COILED_COIL - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_CONCATENATED_SEQUENCE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_CONFLICT - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_CRISPR - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Candidate CRISPR site
TYPE_DISULFIDE_BOND - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_DNA_PROBE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_DOMAIN - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_EDITING_HISTORY_DELETION - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_EDITING_HISTORY_INSERTION - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: A directionless annotation type to record deletions, insertions and replacements of bases in a sequence compared to the original imported sequence.
TYPE_EDITING_HISTORY_REPLACEMENT - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_EXCLUDED_REGION - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Annotations of this type are length 0 annotations between 2 sites, and represent a region of the sequence that has been excluded for some reason, usually for example when viewing a query centric alignment with gaps hidden in the reference sequence.
TYPE_EXON - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_EXPRESSION_LEVEL - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: A type used to represent expression levels (for example when dealing with RNA sequencing data)
TYPE_EXTRACTED_REGION - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: This is an invisible annotation that contains a mapping from the original sequence indices to the current sequence indices.
TYPE_GENE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_HELIX - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_INSERTED_SEQUENCE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_INTRON - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_LIGATION - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_LONG_TERMINAL_REPEAT - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_LOW_QUALITY - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Deprecated.
replaced with SequenceAnnotation.TYPE_TRIMMED.
TYPE_MATURE_PEPTIDE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_MISC_DIFFERENCE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_MISC_FEATURE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_MISC_RNA - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_MOTIF - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_MRNA - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_NCRNA - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_OPTIMIZED_CODON - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: A type used to represent a codon that has been replaced wih an optimized equivalent
TYPE_ORF - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_ORIGIN - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_ORIGIN_OF_REPLICATION - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_OVERHANG - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: A terminal region of a sequence annotated with an annotation of this type is an overhang on one of the strands.
TYPE_PEPTIDE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_POLYA_SIGNAL - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_POLYA_SITE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_POLYLINKER - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_POLYMORPHISM - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Used for any type of variant annotation, for example SNPs or longer variants.
TYPE_PRECURSOR_RNA - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_PRIMER_BIND - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_PRIMER_BIND_REVERSE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_PROMOTER - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_PROTEIN_BIND - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_REPEAT_REGION - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_REPEAT_UNIT - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_RESTRICTION_SITE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_RRNA - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_SEARCH_HIT - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: The type of annotation added to a sequence search result to indicate the region that matched the query sequence
TYPE_SIGNAL_PEPTIDE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_SITE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_SOURCE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_STATISTICS - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: A type used to represent statistical data
TYPE_STRAND - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_TERMINATOR - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_TMRNA - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_TRANSLATED_REGION - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_TRANSMEMBRANE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_TRIMMED - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Regions of a sequence covered by trim annotations are ignored for many operations, including assembly and consensus sequence calculation.
TYPE_TRNA - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_TURN - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_UTR_3 - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_UTR_5 - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_VECTOR_MODERATE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_VECTOR_SEGMENT_OF_SUSPECT_ORIGIN - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_VECTOR_STRONG - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
TYPE_VECTOR_WEAK - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation

U

UNREAD_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField: Visible, non-editable field representing whether a document is unread.
unselectDocuments() - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Unselects any documents currently selected in Geneious.
unzip(File, File, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Extract a zip file.
updateHiddenElement(String, Element, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: updates the contents of a hidden element.
updateProgress(long, long) - Method in class com.biomatters.geneious.publicapi.utilities.ProgressInputStream: Called whenever new data has been read.
updateSequence(int, CharSequence, List<SequenceAnnotation>, NucleotideGraph, boolean) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument: Set new residues and related data for one sequence.
updateSequence(int, CharSequence, List<SequenceAnnotation>, NucleotideGraph, boolean) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
updateSequence(int, CharSequence, List<SequenceAnnotation>, NucleotideGraph, boolean) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument
updateSequence(int, CharSequence, List<SequenceAnnotation>, NucleotideGraph, boolean) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument
URLStreamHandlerManager - Class in com.biomatters.geneious.publicapi.plugin: Deprecated.
Do not call the methods in this class
URLStreamHandlerManager() - Constructor for class com.biomatters.geneious.publicapi.plugin.URLStreamHandlerManager: Deprecated.
URN - Class in com.biomatters.geneious.publicapi.documents: An unmodifiable uniform resource name (URN), intended to serve as persistent, location-independent, resource identifiers.
URN(String, String, String) - Constructor for class com.biomatters.geneious.publicapi.documents.URN: Construct a URN.
URN(URN) - Constructor for class com.biomatters.geneious.publicapi.documents.URN: Constructs a copy of this URN.
URN(String) - Constructor for class com.biomatters.geneious.publicapi.documents.URN: URN factory method.
UrnWithRevisionNumber - Class in com.biomatters.geneious.publicapi.documents: Represents an AnnotatedPluginDocument at a particular revision, via its URN (AnnotatedPluginDocument.getURN()) and revision number (AnnotatedPluginDocument.getRevisionNumber())
UrnWithRevisionNumber() - Constructor for class com.biomatters.geneious.publicapi.documents.UrnWithRevisionNumber
UserEditablePreferences - Class in com.biomatters.geneious.publicapi.plugin: Provides a mechanism for plugins to store advanced user configurable settings as name/value pairs.
UserEditablePreferences() - Constructor for class com.biomatters.geneious.publicapi.plugin.UserEditablePreferences
usesAnnotationsOnInputSequences() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator: Returns true if this annotation generator looks at the annotations on input sequences.

V

ValueAndFrequencyDistribution - Class in com.biomatters.geneious.publicapi.documents.sequence: Provides a sorted distribution of longs and the frequency of each of them.
ValueAndFrequencyDistribution() - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution: Construct a new empty distribution.
ValueAndFrequencyDistribution(ValueAndFrequencyDistribution, ValueAndFrequencyDistribution) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution: Constructs a new distribution by adding 2 distributions together
ValueAndFrequencyDistribution(Element) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution: Construct a new empty distribution from some previously serialized data.
ValueAndFrequencyDistribution.ValueAndFrequency - Class in com.biomatters.geneious.publicapi.documents.sequence: Represents a value and the number of occurrences of the value
ValueAndFrequencyDistribution.ValueAndFrequency(long, long) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.ValueAndFrequencyDistribution.ValueAndFrequency: Construct a new value and frequency
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.components.Dialogs.DialogIcon: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.components.Dialogs.SaveChanges: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBox.ProOnlySuffix: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.databaseservice.CompoundSearchQuery.Operator: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.databaseservice.DatabaseService.SequenceSearchQueryType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.documents.AdditionalSearchContent.Utilities.Filter: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.ActiveLinkSaveBehaviour: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.documents.Condition: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.documents.DocumentField.SequenceType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.documents.DocumentNoteField.Types: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.documents.ExportableDocument.Format: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval.Direction: Returns the enum constant of this type with the specified name.
valueOf(boolean, boolean) - Static method in enum com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval.Direction
valueOf(CharSequence) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: A SequenceCharSequence representing the same sequence of characters as charSequence; It is guaranteed that if charSequence instanceof SequenceCharSequence, charSequence is returned.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument.Alphabet: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument.TaxonomicLevel: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.implementations.PairedReadManager.Orientation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument.OligoType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.Assembler.ContigOutputSupport: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.Assembler.ReferenceSequenceSupport: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.AssemblerInput.DataType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.AutoDetectStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory.ViewPrecedence: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.Geneious.MajorVersion: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions.Category: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions.MainMenu: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.GeneiousService.ServiceStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.Options.Alignment: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.Options.PageChooserType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.Options.RadioOption.DependentPosition: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.SequenceGraph.Location: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceDocumentType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.ComponentLocation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.utilities.CompressionUtilities.CompressionMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.utilities.FileUtilities.RetryPolicy: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.utilities.FileUtilities.TargetExistsAction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.utilities.ImportUtilities.ActionWhenInvalid: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.utilities.ImportUtilities.ImportDocumentType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.biomatters.geneious.publicapi.utilities.StandardIcons: Returns the enum constant of this type with the specified name.
valueOfString(String) - Static method in enum com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument.TaxonomicLevel: Get a TaxonomicLevel from a string
values() - Static method in enum com.biomatters.geneious.publicapi.components.Dialogs.DialogIcon: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.components.Dialogs.SaveChanges: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBox.ProOnlySuffix: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.databaseservice.CompoundSearchQuery.Operator: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.databaseservice.DatabaseService.SequenceSearchQueryType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.documents.AdditionalSearchContent.Utilities.Filter: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument.ActiveLinkSaveBehaviour: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.documents.Condition: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.documents.DocumentField.SequenceType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.documents.DocumentNoteField.Types: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.documents.ExportableDocument.Format: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationInterval.Direction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument.Alphabet: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.documents.types.TaxonomyDocument.TaxonomicLevel: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.implementations.PairedReadManager.Orientation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument.OligoType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.Assembler.ContigOutputSupport: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.Assembler.ReferenceSequenceSupport: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.AssemblerInput.DataType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.DocumentFileImporter.AutoDetectStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory.ViewPrecedence: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.Geneious.MajorVersion: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions.Category: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions.MainMenu: Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousComboBoxPreference: Deprecated.

A list of values, each of which will be displayed as an item in a combo box.
values - Variable in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousRadioButtonPreference: Deprecated.

A list of values, each of which will be displayed as a RadioButton in a set of RadioButtons.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.GeneiousService.ServiceStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.Options.Alignment: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.Options.PageChooserType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.Options.RadioOption.DependentPosition: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.SequenceGraph.Location: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceDocumentType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.ComponentLocation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.utilities.CompressionUtilities.CompressionMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.utilities.FileUtilities.RetryPolicy: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.utilities.FileUtilities.TargetExistsAction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.utilities.ImportUtilities.ActionWhenInvalid: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.utilities.ImportUtilities.ImportDocumentType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.biomatters.geneious.publicapi.utilities.StandardIcons: Returns an array containing the constants of this enum type, in the order they are declared.
valuesFromXML(Element) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Deserializes the current values for these options from XML.
valuesFromXML(Element, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Deserializes the current values for these options from XML.
valuesToXML(String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Serializes the current values for these options to XML for use with a later call to Options.valuesFromXML(org.jdom.Element).
valuesToXML(Geneious.MajorVersion, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options: Serializes the current values for these options to XML for use with a later call to Options.valuesFromXML(org.jdom.Element).
VARIANT_AMINO_ACIDS - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Qualifier used to represent how a SequenceAnnotation.TYPE_POLYMORPHISM has changed from its original value.
VARIANT_CHANGE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Qualifier used to represent how a SequenceAnnotation.TYPE_POLYMORPHISM has changed from its original value.
VARIANT_CHANGE_ARROW - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Used to represent the separating arrow between the original and variant sequence for a SequenceAnnotationQualifier.VARIANT_CHANGE qualifier.
VARIANT_ID - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Qualifier used to represent the database ID of a variant (for example the value may be a dbSNP ID of the form rs1234).
VARIANT_NUCLEOTIDES - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Qualifier used to represent how a SequenceAnnotation.TYPE_POLYMORPHISM has changed from its original value.
VARIANT_REFERENCE_NUCLEOTIDES - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: Qualifier used to represent what the reference sequence was over the interval covered by the annotation
verifyOptionsAreValid() - Method in class com.biomatters.geneious.publicapi.plugin.Options: Override this to have the current contents of options checked (for example String options that allow the user to enter arbitrary text) to make sure they are valid before proceeding.
viewerAppEnvironmentVariableName() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileExporterAndExternalViewer: Name of environment variable which let user specify her preferred external viewer.

W

waitForCompletion() - Method in class com.biomatters.geneious.publicapi.utilities.MultiThreadedProcessingSystem: Waits until all items added using MultiThreadedProcessingSystem.add(Object) have been processed by MultiThreadedProcessingSystem.process(Object) and have returned from MultiThreadedProcessingSystem.finishedProcessing(Object)
waitForGeneiousServiceInitializationToComplete() - Static method in class com.biomatters.geneious.publicapi.plugin.ServiceUtilities: Waits until all GeneiousServices have been initialized.
waitForImageToLoad(Image) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities: Waits until an image has finished loading or returns immediately if it is already loaded.
waitForSearchIndexingToComplete() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: It it permissable for a database to not return documents from a search that have been recently added to the database due to it still indexing those documents for search purposes.
wasKilledByGeneious() - Method in class com.biomatters.geneious.publicapi.utilities.Execution: Returns true if the process was terminated by Geneious due to the Cancelable passed to the constructor requesting that the process execution be canceled.
WEAK_REFERENCED_DOCUMENT_PREFIX - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier: If a qualifier value starts with this prefix, and the remainder of the qualifier value is a URN.toString() of a document, then it is assumed to be a weak reference to that document.
WeakReferenceList<E> - Class in com.biomatters.geneious.publicapi.utilities: Manages a list of WeakReferences, and providing an iterator over the objects which are still strongly referenced.
WeakReferenceList(WeakReferenceList<E>) - Constructor for class com.biomatters.geneious.publicapi.utilities.WeakReferenceList: Constructs a copy of another WeakReferenceList
WeakReferenceList() - Constructor for class com.biomatters.geneious.publicapi.utilities.WeakReferenceList: Constructs an empty WeakReferenceList
WeakSimpleListenerManager - Class in com.biomatters.geneious.publicapi.utilities: Just like a SimpleListenerManager except the references to the listeners are WeakReferences.
WeakSimpleListenerManager() - Constructor for class com.biomatters.geneious.publicapi.utilities.WeakSimpleListenerManager
withNumberOfMappedLocations(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Creates a new sequence identical to this one, except with a different value for ImmutableSequence.getNumberOfMappedLocations()
withNumberOfMappedLocations(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
withOnlyGaps(int) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Gets a char sequence that consists of only gaps.
withoutZeroLengthIntervals() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection
withTerminalGaps(int, CharSequence, int) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Create a new SequenceCharSequence from a CharSequence with the specified terminal gap lengths.
withTrimLengths(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence: Creates a new sequence identical to this one, except with different leading and trailing trim lengths.
withTrimLengths(int, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequenceImplementation
wouldDocumentNameBeUnique(String) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities: Deprecated.
WritableDatabaseService - Class in com.biomatters.geneious.publicapi.databaseservice: Provides a DatabaseService that supports writing documents to it as well as providing a hierarchical folder representation of the database.
WritableDatabaseService() - Constructor for class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService
WritableDatabaseService.SearchResultPropertiesAdjuster - Interface in com.biomatters.geneious.publicapi.databaseservice
write(GeneiousObjectOutputStream, T) - Method in interface com.biomatters.geneious.publicapi.documents.sequence.ExternalSort.Serializer: writes this element to a stream
write(int) - Method in class com.biomatters.geneious.publicapi.utilities.OutputStreamThatCountsBytesWritten
write(byte[]) - Method in class com.biomatters.geneious.publicapi.utilities.OutputStreamThatCountsBytesWritten
write(byte[], int, int) - Method in class com.biomatters.geneious.publicapi.utilities.OutputStreamThatCountsBytesWritten
write(int) - Method in class com.biomatters.geneious.publicapi.utilities.OutputStreamToRandomAccessFile
write(byte[]) - Method in class com.biomatters.geneious.publicapi.utilities.OutputStreamToRandomAccessFile
write(byte[], int, int) - Method in class com.biomatters.geneious.publicapi.utilities.OutputStreamToRandomAccessFile
writeBooleans(DataOutputStream, boolean[], int) - Static method in class com.biomatters.geneious.publicapi.utilities.DataInputOutputUtilities: Writes some boolean values to a stream, using 1 bit per value (rather than 1 byte per value if you use DataOutputStream.writeBoolean(boolean)
writeByte(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectOutputStream
writeByteArray(byte[]) - Method in class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectOutputStream: Writes an array to this stream.
writeInt(int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectOutputStream
writeIntArray(int[]) - Method in class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectOutputStream: Writes an array to this stream.
writeObject(GeneiousObjectOutputStream, NucleotideGraph) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Writes the given graph in a binary format to an output stream (as specified by Serializable) such that it can be recreated using DefaultNucleotideGraph.readObject(GeneiousObjectInputStream).
writeObject(DataOutput, NucleotideGraph) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Equivalent to writeObject(Geneious.getMajorVersion(), out, graph)
writeObject(Geneious.MajorVersion, DataOutput, NucleotideGraph) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph: Writes the given graph in a binary format to an output stream (as specified by Serializable) such that it can be recreated using DefaultNucleotideGraph.readObject(java.io.DataInput).
writeObject(DataOutput, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence
writeObject(Geneious.MajorVersion, DataOutput, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence
writeObject(GeneiousObjectOutputStream) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Writes this annotation to an output stream as defined by Serializable.
writeObject(DataOutput) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Writes this annotation to a DataOutput
writeObject(Geneious.MajorVersion, DataOutput) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation: Writes this annotation to a DataOutput in a form that can potentially be read by old versions of Geneious
writeObject(GeneiousObjectOutputStream, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Writes this sequence to an ObjectOutputStream as specified by Serializable.
writeObject(DataOutput, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Writes this sequence to a DataOutput.
writeObject(Geneious.MajorVersion, DataOutput, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence: Writes this sequence to a DataOutput.
writeObject(GeneiousObjectOutputStream, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Writes this sequence to a stream as specified by Serializable.
writeObject(DataOutput, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Equivalent to writeObject(Geneious.getMajorVersion(), out, progressListener)
writeObject(Geneious.MajorVersion, DataOutput, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument: Writes this sequence to a stream as specified by Serializable.
writeObject(DataOutput, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Writes this manager to a DataOutput
writeObject(Geneious.MajorVersion, DataOutput, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack.Manager: Writes this manager to a DataOutput
writeSequence(SequenceDocument, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectOutputStream: Writes a sequence to this output stream which can be read back using GeneiousObjectInputStream.readSequence()
writeSequence(DataOutput, SequenceDocument, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.DataInputOutputUtilities: Writes a sequence to a DataOutput which can be read back using DataInputOutputUtilities.readSequence(java.io.DataInput)
writeStringOrCompactString(Object) - Method in class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectOutputStream: Writes the given object which may either be a String or a CompactString to this output stream.
writeTextToFile(File, String) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Wrties the given text to a file, overwriting any existing contents of the file.
writeUTF(String) - Method in class com.biomatters.geneious.publicapi.documents.sequence.GeneiousObjectOutputStream
writeUTF(DataOutput, String) - Static method in class com.biomatters.geneious.publicapi.utilities.DataInputOutputUtilities: Writes UTF to a DataOutput without running into the 65K limit normally encountered with DataOutput.writeUTF(String)
writeXmlSerializable(DataOutput, XMLSerializable, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.DataInputOutputUtilities: Writes an XmlSerializable object to a DataOutput which can be read back using DataInputOutputUtilities.readXmlSerializable(java.io.DataInput)

This method lacks many of the optimizations that DataInputOutputUtilities.writeSequence(java.io.DataOutput, com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, jebl.util.ProgressListener) contains.

X

XMLSerializable - Interface in com.biomatters.geneious.publicapi.documents: Interface for handling persistent objects.
XMLSerializable.OldVersionCompatible - Interface in com.biomatters.geneious.publicapi.documents: XMLSerializable classes may implement this to indicate they support serializing to older version formats and potentially deserializing from newer version formats.

This interface should only be implemented by classes bundled with Geneious.
XMLSerializable.VersionSupportType - Enum in com.biomatters.geneious.publicapi.documents: Used for specifying the type of version support when used with XMLSerializable.OldVersionCompatible.getVersionSupport(com.biomatters.geneious.publicapi.documents.XMLSerializable.VersionSupportType)
XMLSerializableWithProgress - Interface in com.biomatters.geneious.publicapi.documents: An extended interface to XMLSerializable to support providing progress (and the ability to cancel) when serializing and deserialing.
XMLSerializationException - Exception in com.biomatters.geneious.publicapi.documents: Represents a problem with XML serialization or deserialization.
XMLSerializationException() - Constructor for exception com.biomatters.geneious.publicapi.documents.XMLSerializationException: Constructs a XMLSerializationException object with no details
XMLSerializationException(String) - Constructor for exception com.biomatters.geneious.publicapi.documents.XMLSerializationException: Constructs a XMLSerializationException object with a specific message.
XMLSerializationException(Throwable) - Constructor for exception com.biomatters.geneious.publicapi.documents.XMLSerializationException: Constructs a XMLSerializationException object with a different Throwable as the underlying cause.
XMLSerializationException(String, Throwable) - Constructor for exception com.biomatters.geneious.publicapi.documents.XMLSerializationException: Constructs a XMLSerializationException object with a specific message and a different Throwable as the underlying cause.
XMLSerializer - Class in com.biomatters.geneious.publicapi.documents: Serialization helper class.
XyzDocument - Class in com.biomatters.geneious.publicapi.implementations.structure: An XYZ molecular structure document.
XyzDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.structure.XyzDocument

Y

YES - Static variable in class com.biomatters.geneious.publicapi.components.Dialogs: An action with "Yes" as its label.
YES_NO - Static variable in class com.biomatters.geneious.publicapi.components.Dialogs: Use this to specify that a dialog should have "Yes" and "No" buttons.
YES_NO_CANCEL - Static variable in class com.biomatters.geneious.publicapi.components.Dialogs: Use this to specify that a dialog should have "Yes", "No" and "Cancel" buttons.

Z

zip(File, File, boolean, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Create a compressed zip containing a file or directory.
zipWithoutCompression(File, File, boolean, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.FileUtilities: Create a zip containing a file or directory without any compression.
zoomIn() - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: A convenience method for zoomIn(0)
zoomIn(int) - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: Changes zoom level to a larger number and notifies listeners that the zoom level has changed.
zoomOut() - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: A convenience method for zoomOut(0)
zoomOut(int) - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: Changes zoom level to a smaller number and notifies listeners that the zoom level has changed.
ZoomPanel - Class in com.biomatters.geneious.publicapi.components: A panel for displaying and setting a zoom level.
ZoomPanel() - Constructor for class com.biomatters.geneious.publicapi.components.ZoomPanel: Calls ZoomPanel(true, true, false, 5).
ZoomPanel(boolean, boolean, boolean, int) - Constructor for class com.biomatters.geneious.publicapi.components.ZoomPanel
zoomTo100Percent() - Method in class com.biomatters.geneious.publicapi.components.ZoomPanel: A convenience method for setZoomLevel(1.0)

_

_add(PluginDocument, Map<String, Object>) - Method in class com.biomatters.geneious.publicapi.databaseservice.CompositeRetrieveCallback: Report back one retrieved document.
_add(AnnotatedPluginDocument, Map<String, Object>) - Method in class com.biomatters.geneious.publicapi.databaseservice.CompositeRetrieveCallback: Report back one retrieved document.
_add(PluginDocument, Map<String, Object>) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: Report back one retrieved document.
_add(AnnotatedPluginDocument, Map<String, Object>) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: Report back one retrieved document.
_addDocumentCopy(AnnotatedPluginDocument, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Implementaion method for WritableDatabaseService.addDocumentCopy(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, jebl.util.ProgressListener) that subclasses should implement.
_addDocumentCopyWithProperties(AnnotatedPluginDocument, ProgressListener, Map<String, Object>) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Deprecated.
use WritableDatabaseService.addDocumentCopyWithProperties(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, jebl.util.ProgressListener, java.util.Map, com.biomatters.geneious.publicapi.documents.URN)
_addDocumentCopyWithProperties(AnnotatedPluginDocument, ProgressListener, Map<String, Object>, URN) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Implementation method for WritableDatabaseService.addDocumentCopyWithProperties(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, jebl.util.ProgressListener, java.util.Map, com.biomatters.geneious.publicapi.documents.URN).
_addReferencedOnlyDocumentCopy(AnnotatedPluginDocument, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: This method is only called from the helper method WritableDatabaseService.duplicateDocumentAndDealWithReferencedDocuments(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, com.biomatters.geneious.publicapi.documents.ElementProvider, java.util.concurrent.atomic.AtomicReference, com.biomatters.geneious.publicapi.documents.URN).
_canRemoveChildFolder(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Sub-classes may override this method to make WritableDatabaseService.canRemoveChildFolder(String) prevent folders from being removed.
_getActionsEnabledWhenServiceSelected() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Sub-classes should override this to provide actions as defined by GeneiousService.getActionsEnabledWhenServiceSelected().
_getExtendedSearchOptions(boolean) - Static method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Get the extended options that most WritableDatabaseServices return from WritableDatabaseService.getExtendedSearchOptions(boolean).
_getFolderViewDocument() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: The implementation method for WritableDatabaseService.getFolderViewDocument().
_getHelp() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Sub-classes should override this to provide help as defined by GeneiousService.getHelp() Ths results of this method are combined with any additional help provided to WritableDatabaseService.addAdditionalHelp(String) to create the results for WritableDatabaseService.getHelp().
_getHiddenFolder(String, boolean) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: The implementation method for WritableDatabaseService.getHiddenFolder(String, boolean)
_getIcons() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Sub-classes should override this to provide icons as defined by GeneiousService.getIcons().
_importDocuments(File, DocumentFileImporter.ImportCallback, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousGridImporter: Import document(s) from a folder.
_isCanceled() - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback: The default implementation always returns false.
_moveDocument(AnnotatedPluginDocument, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Implementation method for WritableDatabaseService.moveDocument(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, jebl.util.ProgressListener) that subclasses should implement.
_removeDocument(AnnotatedPluginDocument, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Implementation method for WritableDatabaseService.removeDocument(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument, jebl.util.ProgressListener) that subclasses should implement.
_retrieve(AnnotatedPluginDocument[], RetrieveCallback, URN[]) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Implementaion method for WritableDatabaseService.retrieve(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback, com.biomatters.geneious.publicapi.documents.URN[]) that subclasses should implement.
_retrieve(URN[], RetrieveCallback) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Implementaion method for WritableDatabaseService.retrieve(com.biomatters.geneious.publicapi.documents.URN[], com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback) that subclasses should implement.
_retrieve(Query, RetrieveCallback, URN[]) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService: Implementaion method for WritableDatabaseService.retrieve(com.biomatters.geneious.publicapi.databaseservice.Query, com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback, com.biomatters.geneious.publicapi.documents.URN[]) that subclasses should implement.
_setImage(Image) - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame
_setImage(Image) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback
_setIndeterminateProgress() - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame
_setIndeterminateProgress() - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback
_setMessage(String) - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame
_setMessage(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback
_setProgress(double) - Method in class com.biomatters.geneious.publicapi.components.ProgressFrame
_setProgress(double) - Method in class com.biomatters.geneious.publicapi.databaseservice.CompositeRetrieveCallback: Set progress, taking progress of current task and completion of previous tasks into account.
_setProgress(double) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback
_setStatus(String, long, boolean, long, long, long) - Method in class com.biomatters.geneious.publicapi.databaseservice.RetrieveCallback
_shutdown() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousService: The implementation method for GeneiousService.shutdown().

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