com.biomatters.geneious.publicapi.plugin

Class SequenceViewerExtension.Factory

java.lang.Object

com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.Factory

Direct Known Subclasses:

SequenceViewerExtension.StatisticsFactory

Enclosing class:

SequenceViewerExtension

public abstract static class SequenceViewerExtension.Factory
extends Object

A type of plugin for creating extensions to the sequence viewer returned from GeneiousPlugin.getSequenceViewerExtensionFactories()

Constructor Summary

Constructors

Constructor and Description
SequenceViewerExtension.Factory()

Method Summary

Methods

Modifier and Type	Method and Description
abstract SequenceViewerExtension	createSequenceViewerExtension(DocumentViewer sequenceViewer, AnnotatedPluginDocument[] documents, SequenceViewerExtension.PropertyRetrieverAndEditor propertyRetriever) Creates an instance of a sequence viewer extension.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SequenceViewerExtension.Factory

public SequenceViewerExtension.Factory()

Method Detail

createSequenceViewerExtension

public abstract SequenceViewerExtension createSequenceViewerExtension(DocumentViewer sequenceViewer,
                                                    AnnotatedPluginDocument[] documents,
                                                    SequenceViewerExtension.PropertyRetrieverAndEditor propertyRetriever)

Creates an instance of a sequence viewer extension.

Parameters:

sequenceViewer - the sequence viewer the extension will be embedded in. There should be no need to for an extension to refer to this directly but it might be useful.

documents - the documents the sequence viewer is referring to. Most of the time these should be ignored since the way the sequence viewer may interpret the data on the documents can vary. In particularly with SequenceListDocuments containing mixtures of amino acid and nucleotide sequences and on CombinedAlignmentAndSequenceDocuments. An implementation should instead use propertyRetriever.getAlphabet(), propertyRetriever.getNumberOfSequences(), and propertyRetriever.isAlignmentOrContig() to decide if it should appear on this particular SequenceViewer.

propertyRetriever - for retrieving data describing the current state of the sequence viewer.

Returns:

a new SequenceViewerExtension instance or null to not create one for this particular view.