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 aGeneiousActionOptions
GeneiousGraphics2D Provides some (but not all) of the functionality ofGraphics2D
, but also provides some extra useful methodsGeneiousGraphics2D.drawStringWithinBounds(String,int,int,int,int,boolean)
GeneiousGraphics2D.drawStringCentred(String, int, int)
The primary reason for the existence of this interface is so thatSequenceGraphs
can be rendered as a circular view in the SequenceViewer correctly.GeneiousGridDocumentOperation.LocationChangedListenerProvider Interface that allowsOperationLocationOptions.LocationChangedListener
s provided by program options to be registered in LocationOptions that are displayed to the userGeneiousPreferences Deprecated. UsePluginPreferences
andGeneiousPlugin.getPluginPreferences()
insteadGeneiousServiceListener Callback used inGeneiousService::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 withOptions.addCustomComponent(com.biomatters.geneious.publicapi.plugin.Options.ComponentCreator)
SequenceViewerExtension.PropertyRetrieverAndEditor.DiscardReferencesCallback Used for indicating that references to values returned fromSequenceViewerExtension.PropertyRetrieverAndEditor.getVisibleAnnotations(PropertyRetrieverAndEditor.DiscardReferencesCallback)
must be discarded. -
Class Summary Class Description ActionProvider May be supplied by aDocumentViewer
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 aDocumentOperation
instead, but that is not recommended.AlignmentOperation.InputProperties Represents the properties of the input to an AlignmentOperationAssembler 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 normalDocumentFileImporter
framework.DocumentAction ADocumentAction
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 documentsDocumentOperation 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 OperationCallbackDocumentOperation.Wrapper Provides a wrapper DocumentOperation that delegates all methods (exceptDocumentOperation.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 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 withPluginDocument
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 toPrintable
which provides additional information and options which also provides useful information when saving to an image.ExtendedPrintable.Factory Provides factory methods for creating ExtendedPrintablesExtendedPrintable.Wrapper Wrapper that delegates all methods to the source ExtendedPrintable.Findable May be supplied by a document viewer (viagetFindable()
) to support textual searching inside the viewer.Findable.FindAllCallback A callback for use withFindable.findAllResults(FindOptions, FindAllCallback, ProgressListener)
Findable.FindOptions User options for a search.Findable.FindResult Represents a single search result feature or locationGeneious 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 ofDocumentOperation
, 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 ofGeneiousPreferences.GeneiousPreference
.GeneiousPreferences.GeneiousPreference Super class for allGeneiousPreferences.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 aDocumentViewer
(viagetNoLongerViewedListener
) to be notified when they are no longer being viewed.OperationLocationOptions AnOptions
that provides the ability to pick between running an Operation on the local computer or on a supportedGeneiousService
.OperationLocationOptions.LocationChangedListener Used to indicate that the value returned fromOperationLocationOptions.getSelectedLocation()
has changed.Options 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 callingOptions.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 boxOptions.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 sideOptions.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 areaOptions.MultipleOptions Stores the multiple options added usingOptions.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 stateOptions.MultipleOptions.setEnabled(boolean)
.Options.Option<ValueType,ComponentType extends javax.swing.JComponent> The base class of all types of options.Options.OptionValue Possible values that aOptions.RadioOption
orOptions.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 ofOptions.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 provideOptions
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 viaSequenceAnnotationGenerator.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 ofSequenceAnnotationGenerator.AnnotationGeneratorResult
where all elements except one are empty results.SequenceAnnotationGenerator.SelectionGrabOption If any option returned fromSequenceAnnotationGenerator.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 (seeSequenceAnnotationGenerator.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 ofSequenceGraph
s 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 annotationSequenceSelection.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 inSequenceListDocuments
.SequenceSelectionWithDocuments This class associates aSequenceSelection
with theList
ofAnnotatedPluginDocument
that it is defined on.SequenceSelectionWithDocuments.ExtractionStrategy Instances of this allow calling code to fine tune howSequenceSelectionWithDocuments.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 fromGeneiousPlugin.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 aSequenceAnnotation
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 acidsSequenceViewerExtension.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 withGeneiousServices
.TestGeneious Provides methods to facilitate writing test cases for Geneious pluginsTreeViewerExtension A tree viewer extension is used for creating a custom controls section in the tree viewer.TreeViewerExtension.Factory The factory class that plugins provide viaGeneiousPlugin.getTreeViewerExtensionFactories()
for creating TreeViewerExtensionsURLStreamHandlerManager Deprecated. Do not call the methods in this classUserEditablePreferences 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 aOptions.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 aCombinedAlignmentAndSequenceDocument
SequenceViewerExtension.ComponentLocation A location in the sequence viewer for the component returned fromSequenceViewerExtension.createComponent()
specified bySequenceViewerExtension.getComponentLocation()
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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 aDocumentFileImporter
that has failed because it has been canceled.RuntimeDocumentOperationException Occasionally some methods that would like to throw aDocumentOperationException
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.