Package com.biomatters.geneious.publicapi.plugin

Provides the GeneiousPlugin interface and plugin related interfaces.

Interface Summary

Interface	Description
DocumentSelectionOption.DoNotRememberInPreferences	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.
GeneiousActionOptions.ShortcutChangeListener	A listener that can be notified when the shortcut changes for a GeneiousActionOptions
GeneiousGraphics2D	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.LocationChangedListenerProvider	Interface that allows OperationLocationOptions.LocationChangedListeners provided by program options to be registered in LocationOptions that are displayed to the user
GeneiousPreferences	Deprecated. Use PluginPreferences and GeneiousPlugin.getPluginPreferences() instead
GeneiousServiceListener	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.
Options.ComponentCreator	An interface for creating components on demand for use with Options.addCustomComponent(com.biomatters.geneious.publicapi.plugin.Options.ComponentCreator)
SequenceViewerExtension.PropertyRetrieverAndEditor.DiscardReferencesCallback	Used for indicating that references to values returned from SequenceViewerExtension.PropertyRetrieverAndEditor.getVisibleAnnotations(PropertyRetrieverAndEditor.DiscardReferencesCallback) must be discarded.

Class Summary

Class	Description
ActionProvider	May be supplied by a DocumentViewer to support standard actions (such as copy and paste) or any additional custom actions.
AlignmentOperation	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.InputProperties	Represents the properties of the input to an AlignmentOperation
Assembler	Allows the implementation of a read mapper, reference assembler or de novo assembler.
Assembler.Callback	Used for assembly algorithms to provide results back to Geneious.
AssemblerInput	Represents the input to an assembly algorithm.
AssemblerInput.Properties	Some properties that briefly summarise what the input will look like.
AssemblerInput.Read	Represents a single read or input contig.
AssemblerInput.ReferenceSequence	Represents a reference sequence in an assembly.
DatabaseFolderImporter	An importer for folders containing files that must be imported as a set, and cannot be handled by the normal DocumentFileImporter framework.
DocumentAction	A DocumentAction performs some operation to modify a document, without creating new documents.
DocumentFileExporter	An exporter writes Geneious documents into external files.
DocumentFileExporterAndExternalViewer	A file exporter with an associated external viewer.
DocumentFileImporter	An importer reads external files and converts the contents to Geneious documents.
DocumentFileImporter.ImportCallback
DocumentFilter	Provides a system for filtering documents
DocumentOperation	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.OperationCallback	Provides a callback facility to DocumentOperations.
DocumentOperation.OperationCallback.Wrapper	Creates a wrapper OperationCallback that delegates all methods to another OperationCallback
DocumentOperation.Wrapper	Provides a wrapper DocumentOperation that delegates all methods (except DocumentOperation.getUniqueId()) to the wrapped operation.
DocumentOperationInput	Represents input to a DocumentOperation.
DocumentSelectionOption	An option to allow the user to select a number of documents of a particular type from their local database.
DocumentSelectionOption.FolderOrDocuments	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	For use with DocumentSelectionOption.setOptionValueCreator(com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption.OptionValueCreator)
DocumentSelectionSignature	Several plugin components (Viewers, Exporters, Operations, Actions) operate on one (or a set of) Geneious documents.
DocumentSelectionSignature.DocumentSelectionSignatureAtom	A signature is a set of Atoms.
DocumentType<T>	Declares one Geneious plugin document type used for associating icons and human readable names with PluginDocument classes.
DocumentViewer	A viewer displays one (or more) Geneious documents to the user.
DocumentViewer.ViewerLocation	Information about the location of a viewer eg.
DocumentViewerFactory	A DocumentViewerFactory creates a DocumentViewer which displays one or more Geneious documents to the user.
DocumentViewerMessageHandler	DocumentViewers occasionally wish to interact with each other.
ExtendedPrintable	An alternative to Printable which provides additional information and options which also provides useful information when saving to an image.
ExtendedPrintable.Factory	Provides factory methods for creating ExtendedPrintables
ExtendedPrintable.Wrapper	Wrapper that delegates all methods to the source ExtendedPrintable.
Findable	May be supplied by a document viewer (via getFindable()) to support textual searching inside the viewer.
Findable.FindAllCallback	A callback for use with Findable.findAllResults(FindOptions, FindAllCallback, ProgressListener)
Findable.FindOptions	User options for a search.
Findable.FindResult	Represents a single search result feature or location
Geneious	General information about the Geneious Prime application.
GeneiousAction	Geneious action items.
GeneiousAction.Divider	A subclass of GeneiousAction which is placed in a toolbar/menu as a divider.
GeneiousAction.SubMenu	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	A subclass of GeneiousAction which is placed in a toolbar/menu as a toggle button or check box menu item.
GeneiousActionOptions	Specifies information (such as the name, description,icon, keyboard shortcut and location) of a menu item or button in Geneious.
GeneiousGridDocumentOperation	A grid-aware version of DocumentOperation, containing many convenience features to simplify the task of creating a grid-aware DocumentOperation.
GeneiousGridDocumentOperation.GridInput	A class describing all the elements needed to run a program on the grid.
GeneiousGridImporter	Imports one or more documents into Geneious from the contents of the given folder.
GeneiousPlugin	The base class for all Geneious plugins.
GeneiousPreferences.GeneiousCheckBoxPreference	A preference for specifying a yes/no (on/off) choice.
GeneiousPreferences.GeneiousComboBoxPreference	A preference for specifying one of a set of values.
GeneiousPreferences.GeneiousDependentPreference	A preference which itself contains a list of GeneiousPreferences.GeneiousPreference.
GeneiousPreferences.GeneiousPreference	Super class for all GeneiousPreferences.GeneiousPreference types.
GeneiousPreferences.GeneiousRadioButtonPreference	A preference for specifying one of a small set of possible values.
GeneiousPreferences.GeneiousStringPreference	A preference for specifying a string.
GeneiousService	A service provides a piece of functionality for the Geneious system.
GeneiousServiceWithPanel	This is a GeneiousService that displays a custom panel in Geneious when the service is selected.
Icons	Stores a set of different sized versions of the same icon.
License	Provides access to the current Geneious user license state, the names of various versions of Geneious, and support for being notified when the license key status changes.
License.PluginLicense	Represents the properties of a license which is used to activate a "pay-for" plugin or feature.
NoLongerViewedListener	May be supplied by a DocumentViewer (via getNoLongerViewedListener) to be notified when they are no longer being viewed.
OperationLocationOptions	An Options that provides the ability to pick between running an Operation on the local computer or on a supported GeneiousService.
OperationLocationOptions.LocationChangedListener	Used to indicate that the value returned from OperationLocationOptions.getSelectedLocation() has changed.
Options	Provides options used by DocumentOperations, SequenceAnnotationGenerators and SequenceGraphs.
Options.BooleanOption	An option that stores a Boolean and is represented graphically as a check box.
Options.ButtonOption	Provides the user with a button which may have actions associated with it by calling Options.ButtonOption.addActionListener(java.awt.event.ActionListener).
Options.ComboBoxOption<ValueType extends Options.OptionValue>	An option that provides the user with a list of options in a combo box
Options.DateOption	An option that stores a date.
Options.DoubleOption	An option that stores an Double and is displayed graphically to the user as a single line text field with a spinner (up and down arrow) on the right-hand side
Options.EditableComboBoxOption	Like a ComboBoxOption, but besides letting the user choose one of the preconfigured default values, also allows arbitrary custom strings to be entered.
Options.ExecutableFileSelectionOption	Provides the user with an executable file name and provides assistance with finding the location of it.
Options.FileSelectionOption	Provides functionality to let the user choose a file.
Options.IntegerOption	An option that stores an Integer and is displayed graphically to the user as a single line text field with a spinner (up and down arrow) on the right-hand side.
Options.LabelOption	An option that is only used for display purposes.
Options.MultipleLineStringOption	An option that stores a String and is displayed to the user as a multiple line text area
Options.MultipleOptions	Stores the multiple options added using Options.addMultipleOptions(String, Options, boolean) and provides methods to access the current values (Options.MultipleOptions.getValues()) and to add change listeners (Options.MultipleOptions.addChangeListener(org.virion.jam.util.SimpleListener) and to change the enabled state Options.MultipleOptions.setEnabled(boolean).
Options.Option<ValueType,ComponentType extends javax.swing.JComponent>	The base class of all types of options.
Options.OptionValue	Possible values that a Options.RadioOption or Options.ComboBoxOption can take on.
Options.RadioOption<ValueType extends Options.OptionValue>	An option that provides the user with a list of radio buttons to select one of
Options.StringOption	An option that stores a String and is displayed graphically to the user as a single line text field.
PasswordOption	An option that stores a user entered password.
PluginPreferences<T extends Options>	Allows a plugin to provide Options based preferences that are displayed in the Geneious Preferences dialog.
PluginUtilities	Provides various functionality to access other installed plug-ins.
PluginUtilities.WritableDatabaseServicesListener	A listener used for notifying when root WritableDatabaseServices are added or removed in Geneious.
SequenceAnnotationGenerator	A SequenceAnnotationGenerator generates annotations on a sequence, set of sequences, or an alignment.
SequenceAnnotationGenerator.AnnotationGeneratorResult	Represents the result of a single sequence from calling an annotation generator via SequenceAnnotationGenerator.generate(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange, jebl.util.ProgressListener, Options)
SequenceAnnotationGenerator.AnnotationGeneratorResult.ResidueAdjustment	An immutable class representing an insertion, deletion, or replacement of residues or bases in a sequence.
SequenceAnnotationGenerator.AnnotationGeneratorResultOnAlignment	Represents the results of running a generator on a single alignment.
SequenceAnnotationGenerator.AnnotationGeneratorResultsOnSingleSequence	An implementation of a List of SequenceAnnotationGenerator.AnnotationGeneratorResult where all elements except one are empty results.
SequenceAnnotationGenerator.SelectionGrabOption	If any option returned from SequenceAnnotationGenerator.getOptions(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.plugin.SequenceAnnotationGenerator.SelectionRange) is a SelectionGrabOption then the sequence viewer will interact with the option such that when the user clicks on the button representing this option, the current selection in the sequence viewer is copied to this option value.
SequenceAnnotationGenerator.SelectionRange	represents a rectangular selection range in a list of sequences, and also behaves like a Linked List in that it provides a link to the next SelectionRange in a chain of selections (see SequenceAnnotationGenerator.SelectionRange.getNext().
SequenceAnnotationGenerator.SingleSequenceResultGenerator	Provides a system for a SequenceAnnotationGenerator to generate results for just a single sequence.
SequenceGraph	A sequence graph is displayed in the SequenceViewer.
SequenceGraph.SequencePropertyRetriever	Provides additional information about the sequence(s) (e.g.
SequenceGraphFactory	A sequence graph factory is used for creating instances of SequenceGraphs every time a new document is viewed in the sequence viewer.
SequenceSelection	Specifies a selection of regions in a sequence, list of sequences, alignment or other sequence containing document.
SequenceSelection.SelectedAnnotation	Represents a single selected annotation
SequenceSelection.SelectionInterval	A contiguous selection of residues in a sequence.
SequenceSelection.SequenceIndex	Represents the index of the selected sequence and the type (so that we can identify which list the index applies to in SequenceListDocuments.
SequenceSelectionWithDocuments	This class associates a SequenceSelection with the List of AnnotatedPluginDocument that it is defined on.
SequenceSelectionWithDocuments.ExtractionStrategy	Instances of this allow calling code to fine tune how SequenceSelectionWithDocuments.getSequences() returns SequenceDocuments from its selection and documents.
SequenceViewerExtension	An extension which provides extra functionality in the sequence/alignment/contig viewer.
SequenceViewerExtension.Factory	A type of plugin for creating extensions to the sequence viewer returned from GeneiousPlugin.getSequenceViewerExtensionFactories()
SequenceViewerExtension.PropertyRetrieverAndEditor	Provides methods for querying the sequence viewer about the status of various things and for requesting that the sequence viewer change its state.
SequenceViewerExtension.SequenceAnnotationWrapper	Wraps a SequenceAnnotation and provides extra information about the location (sequence, track) of the annotation.
SequenceViewerExtension.StateFrequencies<T extends jebl.evolution.sequences.State>	Provides frequencies of nucleotides or amino acids
SequenceViewerExtension.StatisticsFactory	A convenience Factory for creating statistics.
SequenceViewerExtension.StatisticsSection	One or more lines of statistics that show up in the statistics section of the sequence viewer.
ServiceUtilities	Provides various utility functionality dealing with GeneiousServices.
TestGeneious	Provides methods to facilitate writing test cases for Geneious plugins
TreeViewerExtension	A tree viewer extension is used for creating a custom controls section in the tree viewer.
TreeViewerExtension.Factory	The factory class that plugins provide via GeneiousPlugin.getTreeViewerExtensionFactories() for creating TreeViewerExtensions
URLStreamHandlerManager	Deprecated. Do not call the methods in this class
UserEditablePreferences	Provides a mechanism for plugins to store advanced user configurable settings as name/value pairs.
WritableDatabaseServiceTree	A GUI component that lets the user choose a WritableDatabaseService from the root services supplied.

Enum Summary

Enum	Description
Assembler.ContigOutputSupport	Used for indicating whether an assembly algorithm outputs contigs, consensus sequences, or both.
Assembler.ReferenceSequenceSupport	Used for indicating whether an assembly algorithm supports no reference sequence, a single reference sequence, or multiple reference sequences.
AssemblerInput.DataType	The sequencing technology that a sequencing library was generated from.
AssemblerInput.PairedDataType	Represents the type of paired read or mate pair data.
DocumentFileImporter.AutoDetectStatus	Possible results of file type auto detection.
DocumentViewerFactory.ViewPrecedence	Viewer precedence level.
Geneious.MajorVersion	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.
GeneiousActionOptions.Category	The category (if any) which this action fits into.
GeneiousActionOptions.MainMenu	All available menu locations.
GeneiousService.ServiceStatus	Possible states of service.
Options.Alignment	Used the specifying how other options for a Options.RadioOption are layed out.
Options.PageChooserType	An enum listing the different types of child options choosers.
Options.RadioOption.DependentPosition
SequenceGraph.Location
SequenceSelection.SequenceDocumentType	Used for identifying the type of view the selection applies for identifying which list the index applies to in a CombinedAlignmentAndSequenceDocument
SequenceViewerExtension.ComponentLocation	A location in the sequence viewer for the component returned from SequenceViewerExtension.createComponent() specified by SequenceViewerExtension.getComponentLocation()

Exception Summary

Exception	Description
DocumentImportException	An exception thrown when import of document fails due to improper format or unexpected data in file.
DocumentImportException.Canceled	Represents a DocumentFileImporter that has failed because it has been canceled.
RuntimeDocumentOperationException	Occasionally some methods that would like to throw a DocumentOperationException are unable to do so because their API doesn't allow it.
SequenceSelectionWithDocuments.DocumentsInvalidException	Thrown to indicate that a group of documents is not valid to have a SequenceSelectionWithDocuments upon.
SequenceSelectionWithDocuments.SelectedDocumentsModifiedException	Thrown when the selected documents are modified between the moment when the SequenceSelectionWithDocuments is constructed and the documents within it are accessed.

Annotation Types Summary

Annotation Type	Description
MayReturnSlowly	An annotation which indicates a method may take a while to return, so the method should never be called from the Swing thread.
MustReturnPromptly	An annotation which indicates a method should always return promptly (under 50 ms), usually because it may be called from the Swing thread.