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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.
accepts(AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFilter
Returns true if this document is accepted by the filter.
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.
addAll(IntList) - Method in class com.biomatters.geneious.publicapi.utilities.IntList.Array
Adds all values from another IntList to this IntList
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 they appear in the user's local database and so that they become visible in the document table, and returns the newly added documents
addAndReturnGeneratedDocuments(List<AnnotatedPluginDocument>, boolean, List<AnnotatedPluginDocument>, boolean, 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 they appear in the user's local database and so that they become visible in the document table, and returns the newly added documents
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 they appear in the user's 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
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
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.
addChildOptions(String, String, String, Options, double, boolean) - Method in class com.biomatters.geneious.publicapi.plugin.Options
Adds a set of existing Options as child options of this Options with the specified vertical weight.
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.
addColorChooserOption(String, String, Color) - Method in class com.biomatters.geneious.publicapi.plugin.Options
Add an option for letting the user choose a Color
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.
addContigOrScaffoldDocument(SequenceAlignmentDocument, NucleotideSequenceDocument, boolean, boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.Assembler.Callback
Adds a contig or scaffold 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.
addDependentIfNot(Options.Option, ValueType) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option
Similar to #addDependent(Option, Object) except that the dependent is only enabled if the option value is not the value specified here
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.
addDialogClosedListener(Dialogs.DialogClosedListener) - Method in class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions
Add a listener to be notified when a dialog constructed with these options is closed.
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
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
addDocumentSelectionOption(String, String, DocumentSelectionOption.FolderOrDocuments, Set<DocumentType>, DocumentFilter, String, 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 user's local database.
addGeneratedDocument(AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult
Adds a document to the currently selected database folder.
addGeneratedDocuments(List<AnnotatedPluginDocument>, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities
Adds newly generated documents that will appear in the user's 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 they appear in the user's 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 they appear in the user's local database and so that they become visible in the document table.
addGeneratedDocumentsWithLineage(List<AnnotatedPluginDocument>, boolean, WritableDatabaseService, String, List<AnnotatedPluginDocument>, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities
Adds a list of documents that have just been generated to Geneious so that they appear in the user's local database and so that they become visible in the document table.
addGeneratedDocumentsWithLineage(List<AnnotatedPluginDocument>, boolean, WritableDatabaseService, String, List<AnnotatedPluginDocument>, boolean, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities
Adds a list of documents that have just been generated to Geneious so that they appear in the user's 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 user's 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 user's local database.
addHelpButton(String, String) - Method in class com.biomatters.geneious.publicapi.plugin.Options
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.
addHiddenElement(Element, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService.DummyService
 
addHiddenElement(String, Element, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService.DummyService
 
addHistoryEntry(DocumentHistoryEntry) - Method in class com.biomatters.geneious.publicapi.documents.DocumentHistory
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(URN, URN, List<SequenceSelection.SelectionInterval>) - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
Specifies which region in a sequence corresponds to a region in a descendant or parent sequence.
addIntervals(Collection<SequenceAnnotationInterval>) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
adds a collection of intervals to this annotation
addInvolvedIntervals(URN, URN, List<SequenceSelection.SelectionInterval>) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback
Add intervals of document which are involved in this operation.
addInvolvedIntervals(URN, URN, List<SequenceSelection.SelectionInterval>) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentOperation.OperationCallback.Wrapper
 
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.Utilities - Class in com.biomatters.geneious.publicapi.documents
Small helpers for extracting searchable content from XML data.
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.
addLayoutDependent(Options.Option...) - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option
Flags one or more other options so that they appear to the right of this component.
addLayoutDependent(ValueType, Options.Option) - Method in class com.biomatters.geneious.publicapi.plugin.Options.RadioOption
Causes the component for the dependent to appear immediately under the radio button associated with the given OptionValue in any panel returned by this RadioOption.
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).
addNotesTo(AnnotatedPluginDocument, List<DocumentNote>) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentNoteUtilities
Adds a list of document notes to a document
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.
addOptionsToShowOnlyInFirstRow(Options.Option...) - Method in class com.biomatters.geneious.publicapi.plugin.Options.MultipleOptions
Add options that should only show up in the first instance of these multi options.
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 WritableDatabaseService which appears under one of the services returned from PluginUtilities.getWritableDatabaseServiceRoots().
addServiceOption(String, String, WritableDatabaseService, Predicate<GeneiousService>, boolean, boolean, boolean, String, List<WritableDatabaseService>) - Method in class com.biomatters.geneious.publicapi.plugin.Options
Add an option that allows the user to select a WritableDatabaseService 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
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.
addTrackDataFile(String, File) - Method in class com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack
Add a data file to be associated with this track, a copy of which will be stored in the local database and it will not be loaded upon track load.
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.
addUrnVisibleByDefaultTrack(URN) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
Adds a URN to this contig so that any track on this contig/alignment which returns this URN from SequenceTrack.getDocumentVisibleByDefaultOn() will be visible by default.
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(SequenceDocument, 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(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(SequenceDocument, 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.
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.
ALIAS_DOCUMENT_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType
Document type for AliasDocument
AliasDocument - Class in com.biomatters.geneious.publicapi.documents
An alias document created using 'Edit->Paste Alias' or programmatically using AliasDocument.createAlias(AnnotatedPluginDocument).
AliasDocument() - Constructor for class com.biomatters.geneious.publicapi.documents.AliasDocument
Construct a new AliasDocument.
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
AlignmentData(Element) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.AlignmentData
Recreates AlignmentData from a previously serialized AlignmentData
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
ALL - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField
A DocumentField representing an option to search all fields.
ALL_LOCATIONS - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
The name of the qualifier used to display all matching locations for repeat annotations.
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)
allSequencesHaveQuality() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Library
 
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
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.
AnnotationGeneratorResult() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult
Constructs a new AnnotationGeneratorResult with no results.
AnnotationGeneratorResult(List<SequenceAnnotation>) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult
Constructs a new AnnotationGeneratorResult
AnnotationGeneratorResultOnAlignment(List<SequenceAnnotationGenerator.AnnotationGeneratorResult>) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResultOnAlignment
Constructs a new AnnotationGeneratorResultOnAlignment.
AnnotationGeneratorResultsOnSingleSequence(int, int, SequenceAnnotationGenerator.AnnotationGeneratorResult) - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResultsOnSingleSequence
 
annotationsFromXML(Element) - Static method in class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
Return a List of SequenceAnnotations from a JDOM XML Element.
annotationTypeSurvivesTruncation(String) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities
 
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.
applyTracksToAddTo(SequenceTrack.Manager) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.AnnotationGeneratorResult
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
Deprecated.
Geneious no longer respects this as extensions are generally not 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.
Array(int) - Constructor for class com.biomatters.geneious.publicapi.utilities.IntList.Array
Construct a new empty IntList with the given intial capacity
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).
asFastqOrFastaFiles(File, boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Library
Returns this library as a list of between one and three fasta or fastq files.
asFastqOrFastaFiles(File, boolean, boolean, boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Library
Returns this library as a list of between one and three fasta or fastq files.
asGreyedOut(double, float) - Method in class com.biomatters.geneious.publicapi.plugin.Icons
Creates a copy of this Icons with less (or more) saturation and/or a change in alpha.
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
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.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>, List<AssemblerInput.Read>) - Constructor for class com.biomatters.geneious.publicapi.plugin.AssemblerInput
Constructs some assembly input from reads 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 library was generated from.
AssemblerInput.Library - Class in com.biomatters.geneious.publicapi.plugin
A library of reads to be assembled, represented as a single document in Geneious.
AssemblerInput.PairedDataType - Enum in com.biomatters.geneious.publicapi.plugin
Represents the type of paired read or mate pair data.
AssemblerInput.Properties - Class in com.biomatters.geneious.publicapi.plugin
Some properties that briefly summarise what the input will look like.
AssemblerInput.Read - Class in com.biomatters.geneious.publicapi.plugin
Represents a single read or input contig.
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.
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
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.
attemptCloseWhenFailingAnyway(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().
beginAlignHorizontally() - Method in class com.biomatters.geneious.publicapi.plugin.Options
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
between(int, 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 such that if it appears in an alignment with a gap in this region of the given size, will expand to fill that gap.
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.
BIT_SCORE - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField
The Bit-Score for this hit
BooleanOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.BooleanOption
Constructor for XML Serialization.
BooleanOption(String, String, Boolean) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.BooleanOption
Construct a new Boolean option
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(InputStream) - Method in class com.biomatters.geneious.publicapi.utilities.xml.FastSaxBuilder
 
build(Reader) - Method in class com.biomatters.geneious.publicapi.utilities.xml.FastSaxBuilder
 
build(File) - Method in class com.biomatters.geneious.publicapi.utilities.xml.FastSaxBuilder
 
Builder() - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.ImmutableSequence.Builder
 
Builder(boolean, SequenceDocument.Alphabet, boolean) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder
Create a new builder
Builder(boolean, SequenceDocument.Alphabet, boolean, ProgressListener, int) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder
Create a new builder
Builder(boolean, SequenceDocument.Alphabet, boolean, ProgressListener, int, boolean) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListOnDisk.Builder
Create a new builder
Builder() - Constructor for class com.biomatters.geneious.publicapi.implementations.EndGapsManager.Builder
Construct a new Builder.
Builder() - Constructor for class com.biomatters.geneious.publicapi.implementations.PairedReadManager.Builder
button - Variable in class com.biomatters.geneious.publicapi.components.Dialogs.Result
The button clicked by the user (either a String or Dialogs.DialogAction).
Button(GeneiousAction) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.Button
 
ButtonOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption
Constructor for XML Serialization.
ButtonOption(String, String, String, Icon, int) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption
Construct a new ButtonOption.
ButtonOption(String, String, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption
Construct a new ButtonOption with no icon, and center aligned.
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

Cache() - Constructor for class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument.Cache
Constructs a new cache.
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.
Callback() - Constructor for class com.biomatters.geneious.publicapi.plugin.Assembler.Callback
 
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
 
canBeRenamed() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService
Returns whether or not this service can be renamed using WritableDatabaseService.renameFolder(String)
This method is offered because some services can be read only with regards to documents, but allow the folder itself to be renamed.
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
Canceled() - Constructor for exception com.biomatters.geneious.publicapi.plugin.DocumentImportException.Canceled
 
Canceled() - Constructor for exception com.biomatters.geneious.publicapi.plugin.DocumentOperationException.Canceled
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.
canEditDocuments() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService
Returns true if documents in this database can be edited.
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.
canModifySubFolders() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService
Returns whether or not this service allows modifications of its subfolders.
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.
canMoveTo(WritableDatabaseService) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService.DummyService
 
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
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.
capitalize(String) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities
 
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
 
changeAliasesToReferenceNewDocument(AnnotatedPluginDocument, AnnotatedPluginDocument, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.AliasDocument
Changes all aliases in the same database that originalDocument is in that refer to originalDocument to instead refer to newDocument.
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).
CheckBox(String) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBox
 
CheckBox(String, ProOnlyComponents.CheckBox.ProOnlySuffix) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBox
 
CheckBoxMenuItem(GeneiousAction) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.CheckBoxMenuItem
 
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
 
CODON_USAGE_TABLE_DOCUMENT_TYPE - Static variable in class com.biomatters.geneious.publicapi.plugin.DocumentType
Document type for CodonUsageTableDocument
CodonUsageTableDocument - Class in com.biomatters.geneious.publicapi.implementations
A document storing a table of codon usage frequencies.
CodonUsageTableDocument() - Constructor for class com.biomatters.geneious.publicapi.implementations.CodonUsageTableDocument
For deserialization only.
CodonUsageTableDocument(String, int[], AminoAcidState[]) - Constructor for class com.biomatters.geneious.publicapi.implementations.CodonUsageTableDocument
Construct a usage table document from array values
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
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
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
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.
ComboBox(ComboBoxModel) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ComboBox
 
ComboBox(Object[]) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ComboBox
 
ComboBox(Vector<?>) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ComboBox
 
ComboBox() - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ComboBox
 
ComboBox(boolean) - Constructor for class com.biomatters.geneious.publicapi.components.ProOnlyComponents.ComboBox
 
ComboBoxOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption
Constructor for XML Serialization.
ComboBoxOption(String, String, ValueType[], ValueType) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption
Construct a new ComboBoxOption.
ComboBoxOption(String, String, List<? extends ValueType>, ValueType) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ComboBoxOption
Construct a new ComboBoxOption.
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.
concatenateSequences(List<? extends SequenceDocument>, boolean, int, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities
Concatenate a list of sequence documents.
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.
configureParser(XMLReader, SAXHandler) - Method in class com.biomatters.geneious.publicapi.utilities.xml.FastSaxBuilder
 
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.
ConstructorWrapper - Class in com.biomatters.geneious.publicapi.documents.sequence
A wrapper around Constructor that improved performance.
ConstructorWrapper(Constructor) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.ConstructorWrapper
 
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.
containsDocumentAnywhereWithinDatabase(URN) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService.DummyService
 
containsDocumentInThisFolder(URN) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService
Returns true if this folder contains a document with this URN.
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 on the AnnotatedPluginDocument that wraps it

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
copyDocumentFields(PluginDocument, AbstractPluginDocument, boolean) - Static method in class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities
Copy important document fields (such as organism, taxonomy and common name) from any PluginDocument to any AbstractPluginDocument
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.
copyNotes(AnnotatedPluginDocument, AnnotatedPluginDocument) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentNoteUtilities
Copies all document notes from one document to another
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.
Coverage(double, int, int, boolean) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Coverage
 
Coverage(double, double, double, boolean) - Constructor for class com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Coverage
 
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.
createAlias(AnnotatedPluginDocument) - Static method in class com.biomatters.geneious.publicapi.documents.AliasDocument
 
createAliases(List<AnnotatedPluginDocument>) - Static method in class com.biomatters.geneious.publicapi.documents.AliasDocument
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
createAnnotatedPluginDocument(PluginDocument, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities
Creates an AnnotatedPluginDocument from a PluginDocument.
createAnnotatedPluginDocument(PluginDocument, URN, ProgressListener) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities
Creates an AnnotatedPluginDocument from a PluginDocument with a specific URN.
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
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.
createChildFolder(String) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService.DummyService
 
createCompactCharSequence(CharSequence) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceBuilder
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.PasswordOption
 
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(boolean) - 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.
createFormattedPotentialRestrictionSiteQualifier(String, String, int, int, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Create a formatted potential restriction site value for Modified or Original qualifier
createFromAnnotation(int, SequenceAnnotation, int, boolean, SequenceAnnotationGenerator.SelectionRange) - Static method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange
Create a SelectionRange from an annotation with at least one non-empty interval.
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.
createHyperlink(String, String) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities
Returns a hyperlink from the given text to the url for use in html, by surrounding the linkText with an href tag.
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.
createImageFromIcon(Icon) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities
Creates an image from the given icon.
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.
createMaskedAnnotation(int, int) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
Creates a new SequenceAnnotation.TYPE_MASKED annotation
createNewDocumentByTransformingSequences(SequenceDocument.Alphabet, SequenceDocument.Transformer, ProgressListener) - Method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
createNewDocumentByTransformingSequences(SequenceListDocument, SequenceDocument.Alphabet, SequenceDocument.Transformer, ProgressListener, boolean) - Static 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 sequenceListDocument.
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.
createNewDocumentsByTransformingSequences(List<AnnotatedPluginDocument>, SequenceDocument.Transformer, ProgressListener, String, 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.
createOptionValueForDocument(AnnotatedPluginDocument) - Method in class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.OptionValueCreator
 
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.
createSequenceCopyAdjustedForGapInsertion(SequenceDocument, CharSequence, boolean) - 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
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
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
createUrnForThisDatabase() - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService
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().
CustomToolbarComponent(String, JComponent, double, boolean, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar.CustomToolbarComponent
Defines custom toolbar component properties

D

DATA_TYPE_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField
Sequencing platform that produced the data (labeled as 'Read Technology' in the UI)
DATABASE_LOCATION_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField
A field used when searching a WritableDatabaseService to indicate which folder the document is in.
DatabaseFolderImporter - Class in com.biomatters.geneious.publicapi.plugin
An importer for folders containing files that must be imported as a set, and cannot be handled by the normal DocumentFileImporter framework.
DatabaseFolderImporter() - Constructor for class com.biomatters.geneious.publicapi.plugin.DatabaseFolderImporter
 
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
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
DefaultHyperlinkListener.SerializableRunnable - Interface in com.biomatters.geneious.publicapi.components
defaultLinuxViewers() - Method in class com.biomatters.geneious.publicapi.plugin.DocumentFileExporterAndExternalViewer
Linux application name(s) of viewers.
DefaultModelWhereSetSelectedItemDoesntFireContentsChanged() - Constructor for class com.biomatters.geneious.publicapi.components.GComboBox.DefaultModelWhereSetSelectedItemDoesntFireContentsChanged
 
DefaultModelWhereSetSelectedItemDoesntFireContentsChanged(Object[]) - Constructor for class com.biomatters.geneious.publicapi.components.GComboBox.DefaultModelWhereSetSelectedItemDoesntFireContentsChanged
 
DefaultModelWhereSetSelectedItemDoesntFireContentsChanged(Vector<?>) - Constructor for class com.biomatters.geneious.publicapi.components.GComboBox.DefaultModelWhereSetSelectedItemDoesntFireContentsChanged
 
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.
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.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.
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.
DialogAction(String) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogAction
 
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
 
dialogClosed(Object) - Method in interface com.biomatters.geneious.publicapi.components.Dialogs.DialogClosedListener
 
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
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
DialogOptions(String[], String) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions
 
DialogOptions(Dialogs.DialogAction[], String) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions
 
DialogOptions(String[], String, Component) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions
 
DialogOptions(Dialogs.DialogAction[], String, Component) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions
 
DialogOptions(String[], String, Component, Dialogs.DialogIcon) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions
 
DialogOptions(Dialogs.DialogAction[], String, Component, Dialogs.DialogIcon) - Constructor for class com.biomatters.geneious.publicapi.components.Dialogs.DialogOptions
 
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.DialogClosedListener - Interface in com.biomatters.geneious.publicapi.components
A listener to be notified when a dialog is closed.
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 specifies all the options for displaying a dialog.
Dialogs.Result - Class in com.biomatters.geneious.publicapi.components
The result of showing an "apply to all" dialog.
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).
DIFFERENTIAL_EXPRESSION_ABSOLUTE_CONFIDENCE_QUALIFIER - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for differential expression absolute confidence
DIFFERENTIAL_EXPRESSION_ADJUSTED_P_VALUE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for differential expression adjust p-value
DIFFERENTIAL_EXPRESSION_BASE_MEAN - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for differential expression base mean
DIFFERENTIAL_EXPRESSION_CONFIDENCE_QUALIFIER - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for differential expression confidence
DIFFERENTIAL_EXPRESSION_LOG2_RATIO_QUALIFIER - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for differential expression log base 2 ratio
DIFFERENTIAL_EXPRESSION_LOG_FOLD_STANDARD_ERROR_QUALIFIER - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for differential expression log fold standard error
DIFFERENTIAL_EXPRESSION_METHOD - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for the differential expression method used
DIFFERENTIAL_EXPRESSION_P_VALUE - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for differential expression p-value
DIFFERENTIAL_EXPRESSION_RATIO_QUALIFIER - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for differential expression expression ratio
DIFFERENTIAL_EXPRESSION_WALD_STAT - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for differential expression Wald statistic
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 on the AnnotatedPluginDocument that wraps it.

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.
displayCustomizeToolbarDialog() - Method in class com.biomatters.geneious.publicapi.components.GeneiousActionToolbar
Displays a toolbar allowing the user to choose which items appear in this toolbar.
displayDocumentSearchDialog(String, DocumentSearchCache, Set<DocumentType>, DocumentFilter, String, List<AnnotatedPluginDocument>, DocumentSelectionOption.FolderOrDocuments, List<DocumentField>, boolean, boolean, JComponent) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities
Display a dialog allowing the user to choose document(s) from their local database (or connected shared databases).
Divider() - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousAction.Divider
 
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_SEARCHING_ANNOTATION_NAME_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField
Field used when searching a DatabaseService for documents containing annotations matching a given name.
DOCUMENT_SEARCHING_ANNOTATION_TYPE_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField
Field used when searching a DatabaseService for documents containing annotations matching a given type.
DOCUMENT_SEARCHING_ANNOTATIONS_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField
Field used when searching a DatabaseService for documents containing annotations whose name, type, or qualifiers match given text.
DOCUMENT_SEARCHING_TRACKS_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField
Field used when searching a DatabaseService for documents containing sequence tracks whose name or qualifiers match given text.
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
 
DocumentFilter - Class in com.biomatters.geneious.publicapi.plugin
Provides a system for filtering documents
DocumentFilter() - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentFilter
 
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.
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
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.Wrapper - Class in com.biomatters.geneious.publicapi.plugin
Creates a wrapper OperationCallback that delegates all methods to another OperationCallback
DocumentOperation.Wrapper - Class in com.biomatters.geneious.publicapi.plugin
Provides a wrapper DocumentOperation that delegates all methods (except DocumentOperation.getUniqueId()) to the wrapped 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.
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.DoNotRememberInPreferences - Interface in com.biomatters.geneious.publicapi.plugin
An interface that documents used in a DocumentSelectionOption may implement so that the option doesn't cache their instance and reuse it on future instances of these options.
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.OptionValueCreator - Class in com.biomatters.geneious.publicapi.plugin
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.
DocumentSelectionSignatureAtom(Class, int, int) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature.DocumentSelectionSignatureAtom
constructor.
DocumentsInvalidException(String) - Constructor for exception com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.DocumentsInvalidException
Constructs a new instance of this exception with the given message
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.
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).
DONT_SHOW_AGAIN - Static variable in class com.biomatters.geneious.publicapi.components.Dialogs
DoubleOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.DoubleOption
Constructor for XML Serialization.
DoubleOption(String, String, Double) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.DoubleOption
Construct a new Double option
DoubleOption(String, String, Double, Double, Double) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.DoubleOption
Construct a new Double option
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
DummyService(String, String, Icons) - Constructor for class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService.DummyService
Construct a new dummy service that provides no functionality apart from a name and icons
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
duplicateDocumentThrowingDocumentOperationExceptionOnFailure(AnnotatedPluginDocument, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities
Create a duplicate of document.

E

E_VALUE_FIELD - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField
The eValue for this hit
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.
EDITED_NUCLEOTIDE_QUALITY - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph
The quality score assigned to a nucleotide which is edited in a sequence with quality.
EDITING_HISTORY - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup
EDITING_HISTORY_ORIGINAL_BASES - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
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.
ElementHandler() - Constructor for class com.biomatters.geneious.publicapi.utilities.xml.PluginDocumentXmlCollection.ElementHandler
 
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.
EMPTY - Static variable in class com.biomatters.geneious.publicapi.utilities.IntList
An empty immutable IntList
enableValues - Variable in class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousDependentPreference
Deprecated.
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
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 (100 MB in the current implementation) to be safe, and if not throws an XMLSerializationException

Warning: Do not use this method inside a loop or it can cause performance issues.
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.Icons
 
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.SelectedAnnotation
 
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
 
equals(Object) - Method in class com.biomatters.geneious.publicapi.utilities.IntList
 
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.
escapeHtmlCharacters(String) - Static method in class com.biomatters.geneious.publicapi.utilities.StringUtilities
Escapes all of the HTML reserved characters in the given string, replacing them with equivalent HTML entities.
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
 
ExecutableFileSelectionOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ExecutableFileSelectionOption
Constructor for XML Serialization.
ExecutableFileSelectionOption(String, String, String, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.ExecutableFileSelectionOption
Construct a new ExecutableFileOption.
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.
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(File, ProgressListener, Geneious.MajorVersion, Geneious.MajorVersion, Geneious.MajorVersion, List<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.
EXPRESSION_FPKM - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for expression FPKM (fragments per kilobase million)
EXPRESSION_RAW_FRAGMENT_COUNT - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for expression raw fragment count
EXPRESSION_RAW_READ_COUNT - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for expression raw read count
EXPRESSION_RAW_TRANSCRIPT_COUNT - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for expression raw transcript count
EXPRESSION_RPKM - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for expression RPKM (reads per kilobase million)
EXPRESSION_TPM - Static variable in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
Qualifier name for expression TPM (transcripts per million)
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.
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
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.
ExtractionOptions(SequenceExtractionUtilities.ExtractionOptions) - Constructor for class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions
Constructs some new extraction options identical to the given ones.
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.
ExtractionOptions(List<SequenceAnnotationInterval>) - Constructor for class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions
Construct the extraction options from a list of intervals.
ExtractionOptions(SequenceAnnotationInterval...) - Constructor for class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions
Construct the extraction options from a list of intervals.
ExtractionOptions(Interval...) - Constructor for class com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions
Construct the extraction options from a list of intervals.
ExtractionStrategy() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceSelectionWithDocuments.ExtractionStrategy
 
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.
extractSelectedAnnotations() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor
Extracts the selected annotations into new document(s)

This method may only be invoked from the Swing thread

F

Factory() - Constructor for class com.biomatters.geneious.publicapi.databaseservice.Query.Factory
 
Factory() - Constructor for class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.Factory
 
Factory() - Constructor for class com.biomatters.geneious.publicapi.plugin.TreeViewerExtension.Factory
 
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
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.
FieldWithName - Interface in com.biomatters.geneious.publicapi.documents
Interface implemented by fields that have a name.
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.
FileSelectionOption(Element) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption
Constructor for XML Serialization.
FileSelectionOption(String, String, String, String[], String, FilenameFilter) - Constructor for class com.biomatters.geneious.publicapi.plugin.Options.FileSelectionOption
Construct a new FileSelectionOption.
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.
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).
fireListenersToFireAfterChangingAllValues() - Method in class com.biomatters.geneious.publicapi.plugin.Options
Called in conjunction with Options.initializeListenersToFireAfterChangingAllValues() to delay firing of listeners added to this Options and its child Option objects until such time as this method is called.
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
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
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
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
 
FolderOrDocuments(WritableDatabaseService) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.FolderOrDocuments
Create a FolderOrDocuments for a folder selection
FolderOrDocuments(List<AnnotatedPluginDocument>) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.FolderOrDocuments
Create a FolderOrDocuments for a selection of documents
FolderOrDocuments(AnnotatedPluginDocument) - Constructor for class com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.FolderOrDocuments
Create a FolderOrDocuments for a selection of one document
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.
followAlias(AnnotatedPluginDocument) - Static method in class com.biomatters.geneious.publicapi.documents.AliasDocument
If the provided document is an alias, follows this alias to the original document
followAliases(List<AnnotatedPluginDocument>, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.AliasDocument
followHyperlink(String) - Static method in class com.biomatters.geneious.publicapi.components.DefaultHyperlinkListener
Follows a hyperlink, either by opening it in an external web browser (if it is a URL), or selecting the document (if it is a Geneious URN)
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.
forAnnotation(SequenceAnnotation, int, int, boolean) - Static method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.SequenceAnnotationWrapper
Wraps a SequenceAnnotation and provides extra information about the location (sequence, track) of the annotation.
forAnnotations(List<SequenceSelection.SelectedAnnotation>) - Static method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection
 
forBothSequenceTypes(List<NucleotideSequenceDocument>, List<AminoAcidSequenceDocument>) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument
Construct a new DefaultSequenceListDocument.
forBothSequenceTypes(SequenceDocument...) - 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.
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
 
fromString(String) - Static method in class com.biomatters.geneious.publicapi.utilities.IntList
Creates an IntList from its IntList.toString() representation
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.AliasDocument
 
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.CodonUsageTableDocument
 
fromXML(Element) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
 
fromXML(Element, ProgressListener) - Method in class com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument
Deserializes this document with progress.
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.implementations.TextDocument
 
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
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
 
GC_PERCENT - Static variable in class com.biomatters.geneious.publicapi.documents.DocumentField
The GC percentage of a nucleotide sequence, contig, or alignment.
GCheckBox - Class in com.biomatters.geneious.publicapi.components
Like a JCheckBox except Is not opaque (calls setOpaque(false) in the constructor) Adds GCheckBox.setSmall(boolean) Works around a preferred size bug on High DPI displays under Java 9
GCheckBox() - Constructor for class com.biomatters.geneious.publicapi.components.GCheckBox
See JCheckBox.JCheckBox()
GCheckBox(Icon) - Constructor for class com.biomatters.geneious.publicapi.components.GCheckBox
See JCheckBox.JCheckBox(Icon)
GCheckBox(Icon, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.GCheckBox
See JCheckBox.JCheckBox(Icon, boolean)
GCheckBox(String) - Constructor for class com.biomatters.geneious.publicapi.components.GCheckBox
See JCheckBox.JCheckBox(String)
GCheckBox(Action) - Constructor for class com.biomatters.geneious.publicapi.components.GCheckBox
See JCheckBox.JCheckBox(Action)
GCheckBox(String, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.GCheckBox
See JCheckBox.JCheckBox(String, boolean)
GCheckBox(String, Icon) - Constructor for class com.biomatters.geneious.publicapi.components.GCheckBox
See JCheckBox.JCheckBox(String, Icon)
GCheckBox(String, Icon, boolean) - Constructor for class com.biomatters.geneious.publicapi.components.GCheckBox
See JCheckBox.JCheckBox(String, Icon, boolean)
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
If this is a non-editable ComboBox, it is strongly recommended that your model inherits from GComboBox.DefaultModelWhereSetSelectedItemDoesntFireContentsChanged rather than DefaultComboBoxModel, as the latter has performance issues when dealing with large numbers of list items.
GComboBox(Object[]) - Constructor for class com.biomatters.geneious.publicapi.components.GComboBox
 
GComboBox(Collection<?>) - Constructor for class com.biomatters.geneious.publicapi.components.GComboBox
Creates a Combobox by converting the collection to an array and delegating to GComboBox.GComboBox(Object[])
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.AlternativeDropDownTextProvider - 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, GComboBox.AlternativeDropDownTextProvider.getDropDownText(boolean) will be called to obtain the displayed text instead of Component.toString() Note: A GComboBox which has items implementing this interface is not mutable.
GComboBox.DefaultModelWhereSetSelectedItemDoesntFireContentsChanged - Class in com.biomatters.geneious.publicapi.components
ComboBoxModel which extends DefaultComboBoxModel but which fixes performance issues when iterating through selected items.
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 was written to works around Java bug 6406218 That bug no longer exists, but tbis class is being left in as a simple proxy to JEditorPane so as not change the public API
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 Prime 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.
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.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.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.
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.
GeneiousCheckBoxPreference(String, String, boolean) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousCheckBoxPreference
Deprecated.
 
GeneiousComboBoxPreference(String, String, Object[], Object) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousComboBoxPreference
Deprecated.
 
GeneiousDependentPreference(String, String, GeneiousPreferences.GeneiousPreference[], GeneiousPreferences.GeneiousPreference, List<String>) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousDependentPreference
Deprecated.
 
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.LocationChangedListenerProvider - Interface in com.biomatters.geneious.publicapi.plugin
Interface that allows OperationLocationOptions.LocationChangedListeners provided by program options to be registered in LocationOptions that are displayed to the user
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
GeneiousPreferences.GeneiousCheckBoxPreference - Class in com.biomatters.geneious.publicapi.plugin
Deprecated.
A preference for specifying a yes/no (on/off) choice.
GeneiousPreferences.GeneiousComboBoxPreference - Class in com.biomatters.geneious.publicapi.plugin
Deprecated.
A preference for specifying one of a set of values.
GeneiousPreferences.GeneiousDependentPreference - Class in com.biomatters.geneious.publicapi.plugin
Deprecated.
A preference which itself contains a list of GeneiousPreferences.GeneiousPreference.
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.GeneiousStringPreference - Class in com.biomatters.geneious.publicapi.plugin
Deprecated.
A preference for specifying a string.
GeneiousRadioButtonPreference(String, String, String[], String) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousRadioButtonPreference
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
 
GeneiousStringPreference(String, String, String) - Constructor for class com.biomatters.geneious.publicapi.plugin.GeneiousPreferences.GeneiousStringPreference
Deprecated.
 
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, and generated documents 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
generateAnnotations(SequenceAnnotationGenerator.SelectionRange, ProgressListener, Options, List<AnnotatedPluginDocument>) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator
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
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(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(Icons, Icons...) - Static method in class com.biomatters.geneious.publicapi.components.OverlayIcons
Return an Icons that overlays one or more Icons on top of a base Icons.
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.
getAbsoluteMouseLocation() - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities
Returns the Point that represents the coordinates of the mouse pointer on the screen.
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.
getAdditionalInformation() - Method in class com.biomatters.geneious.publicapi.documents.OperationRecordDocument
 
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
getAdditionalPerDocumentXml(AnnotatedPluginDocument, List<String>, boolean, ProgressListener) - Method in class com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService
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
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.
getAliasedUrn(AnnotatedPluginDocument) - Static method in class com.biomatters.geneious.publicapi.documents.AliasDocument
Retrieves the URN of a document aliased by this document without retrieving it from persistent storage
getAlignment() - Method in class com.biomatters.geneious.publicapi.plugin.Options.RadioOption
 
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
getAlignmentHiddenQualifierName(SequenceDocument.Alphabet, boolean, String, String) - Static method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
Returns the name of an hidden (SequenceAnnotationQualifier.HIDDEN_PREFIX) annotation qualifier that can be used for storing a single sequence that will appear in the alignments returned from SequenceAnnotation.getAlignmentsFromHiddenQualifiers().
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
 
getAlignmentsFromHiddenQualifiers() - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
All alignments that can be created from hidden qualifiers returned from SequenceAnnotation.getAlignmentHiddenQualifierName(SequenceDocument.Alphabet, boolean, String, String).
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.
getAlphabet(AnnotatedPluginDocument...) - Static method in class com.biomatters.geneious.publicapi.utilities.SequenceUtilities
 
getAminoAcid(CodonState) - Method in class com.biomatters.geneious.publicapi.implementations.CodonUsageTableDocument
Get the amino acid translation for a given codon.
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.
getAnnotatedPluginDocuments() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput
 
getAnnotatedPluginDocuments() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.PropertyRetrieverAndEditor
Get the current AnnotatedPluginDocuments of all of the sequences being viewed by this viewer instance.
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 and only one
getAnnotation() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectedAnnotation
 
getAnnotationAdjustedForDeletion(int, int, boolean, int) - Method in class com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation
getAnnotationAdjustedForDeletion(int, CharSequence, 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
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
getAnnotationIndex() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection.SelectedAnnotation
 
getAnnotationQualifiersToShowAfterNameForRealTimeAnnotations(Options) - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator
If this is a real time annotation generator (i.e.
getAnnotations() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection
 
getAnnotationSequenceIndex() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceSelection
Get the sequence index of the selected annotation if there is single selected 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
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
 
getAT() - Method in class com.biomatters.geneious.publicapi.implementations.sequence.NucleotideCounter
 
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
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
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.
getClipboardContents(DataFlavor) - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities
Get the data on the system clipboard for the given flavor or null if it's not available or there was a problem accessing the clipboard.
getClipboardTransferable() - Static method in class com.biomatters.geneious.publicapi.utilities.GuiUtilities
Get the current Transferable on the system clipboard or null if there was a problem accessing the clipboard.
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()
getColoredImage(Image, Color) - Static method in class com.biomatters.geneious.publicapi.utilities.IconUtilities
Moves the colors in this image towards the given color.
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
 
getComponentWithUnitsAndHelpButton() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option
 
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
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.
getCount(CodonState) - Method in class com.biomatters.geneious.publicapi.implementations.CodonUsageTableDocument
Get the absolute count for a given codon.
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.AliasDocument
 
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.CodonUsageTableDocument
 
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.
getCreationDate() - Method in class com.biomatters.geneious.publicapi.implementations.TextDocument
 
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.
getDatabaseFolderImporter(String) - Static method in class com.biomatters.geneious.publicapi.plugin.PluginUtilities
get the DatabaseFolderImporter with the given unique ID.
getDatabaseFolderImporters() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin
get the database importers provided by this plugin.
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
getDatabaseTypeDescription() - Method in class com.biomatters.geneious.publicapi.plugin.DatabaseFolderImporter
 
getDataType() - Method in class com.biomatters.geneious.publicapi.plugin.AssemblerInput.Library
 
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.
getDependencies() - Method in class com.biomatters.geneious.publicapi.plugin.GeneiousPlugin
 
getDependentChildOptions() - Method in class com.biomatters.geneious.publicapi.plugin.Options.ButtonOption
 
getDependents() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option
 
getDependentsIfNot() - Method in class com.biomatters.geneious.publicapi.plugin.Options.Option
 
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.databaseservice.WritableDatabaseService.DummyService
 
getDescription() - Method in class com.biomatters.geneious.publicapi.documents.AliasDocument
 
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() - Method in class com.biomatters.geneious.publicapi.implementations.CodonUsageTableDocument
 
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.implementations.TextDocument
 
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.
getDirection() - Method in class com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange
 
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.AliasDocument
 
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.CodonUsageTableDocument
 
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
 
getDisplayableFields() - Method in class com.biomatters.geneious.publicapi.implementations.TextDocument
 
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.DummyService
 
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
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.DummyService
 
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
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
getDocuments(boolean) - Method in class com.biomatters.geneious.publicapi.documents.DocumentSearchCache
 
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
 
getDocumentsByURN(List<URN>, boolean) - Static method in class com.biomatters.geneious.publicapi.documents.DocumentUtilities
Fetches the specified documents from either in memory or fro