com.biomatters.geneious.publicapi.plugin

Class SequenceViewerExtension.StatisticsFactory

java.lang.Object

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

com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsFactory

Enclosing class:

SequenceViewerExtension

public abstract static class SequenceViewerExtension.StatisticsFactory
extends SequenceViewerExtension.Factory

A convenience Factory for creating statistics. A plugin can return a StatisticsFactory directly from GeneiousPlugin.getSequenceViewerExtensionFactories()

Since:

API 4.700 (Geneious 7.0.0)

Constructor Summary

Constructors

Constructor and Description
SequenceViewerExtension.StatisticsFactory()

Method Summary

Methods

Modifier and Type	Method and Description
SequenceViewerExtension	createSequenceViewerExtension(DocumentViewer sequenceViewer, AnnotatedPluginDocument[] documents, SequenceViewerExtension.PropertyRetrieverAndEditor propertyRetriever) Creates an instance of a sequence viewer extension.
abstract List<SequenceViewerExtension.StatisticsSection>	createStatistics(SequenceViewerExtension.PropertyRetrieverAndEditor propertyRetriever, ProgressListener progressListener) Generates one or more sections of statistics to be displayed in the statistics controls section.
String	getUniqueId()

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceViewerExtension.StatisticsFactory

public SequenceViewerExtension.StatisticsFactory()

Method Detail

createSequenceViewerExtension

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

Description copied from class: SequenceViewerExtension.Factory

Creates an instance of a sequence viewer extension.

Specified by:

createSequenceViewerExtension in class SequenceViewerExtension.Factory

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.

createStatistics

public abstract List<SequenceViewerExtension.StatisticsSection> createStatistics(SequenceViewerExtension.PropertyRetrieverAndEditor propertyRetriever,
                                                               ProgressListener progressListener)

Generates one or more sections of statistics to be displayed in the statistics controls section.

Parameters:

propertyRetriever - for obtaining properties about the current state of the sequence viewer. The implementation should take the selection (available via getSelectionForStatistics) into account

progressListener - for reporting progress and checking if statistics should be cancelled. It is important that an implementation cancel promptly or it can hang the sequence viewer when the user tries to edit.

Returns:

the statistics or an empty list to provide no statistics

getUniqueId

public String getUniqueId()

Returns:

a unique ID for this extension type. The default implementation returns the fully qualified class name.