Package com.biomatters.geneious.publicapi.plugin

Class SequenceViewerExtension

java.lang.Object

com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension

public abstract class SequenceViewerExtension
extends java.lang.Object

An extension which provides extra functionality in the sequence/alignment/contig viewer.

The Sequence Viewer is the plugin bundled with Geneious that is responsible for providing the "Sequence View", "Alignment View", "Contig View".

Extensions can provide

• a custom component (via getComponent()) which can be positioned below or adjacent to the main sequence viewer display or within annotation or statistics controls
• custom statistics (via getStatistics)
• sequence viewer toolbar actions (via getToolbarActions())

Examples of sequence viewer extensions in Geneious are the annotations table and many of the statistics in the sequence viewer (and maybe one day actions such as the extract and translate buttons)

A SequenceViewerExtension is returned from SequenceViewerExtension.Factory.createSequenceViewerExtension(DocumentViewer, com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], PropertyRetrieverAndEditor)

Since:

API 4.60 (Geneious 5.6.0)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SequenceViewerExtension.ComponentLocation	A location in the sequence viewer for the component returned from createComponent() specified by getComponentLocation()
static class	SequenceViewerExtension.Factory	A type of plugin for creating extensions to the sequence viewer returned from GeneiousPlugin.getSequenceViewerExtensionFactories()
static class	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.
static class	SequenceViewerExtension.SequenceAnnotationWrapper	Wraps a SequenceAnnotation and provides extra information about the location (sequence, track) of the annotation.
static class	SequenceViewerExtension.StateFrequencies<T extends jebl.evolution.sequences.State>	Provides frequencies of nucleotides or amino acids
static class	SequenceViewerExtension.StatisticsFactory	A convenience Factory for creating statistics.
static class	SequenceViewerExtension.StatisticsSection	One or more lines of statistics that show up in the statistics section of the sequence viewer.

Constructor Summary

Constructors

Constructor	Description
SequenceViewerExtension()

Method Summary

Modifier and Type	Method	Description
void	addComponentLocationChangedListener(org.virion.jam.util.SimpleListener listener)	Adds a listener to be notified when the value returned from getComponentLocation() changes
void	addComponentPositionActions(GeneiousActionToolbar toolbar, SequenceViewerExtension.ComponentLocation... locations)	Adds little buttons to a toolbar to control the location (see getComponentLocation()) of the component (see getComponent()) in the sequence viewer.
void	addComponentPositionPopInOrOutAction(GeneiousActionToolbar toolbar, SequenceViewerExtension.ComponentLocation inLocation, SequenceViewerExtension.ComponentLocation outLocation)	Adds a little button to the toolbar to control the location (see getComponentLocation()) of the component (see getComponent()) in the sequence viewer.
protected javax.swing.JComponent	createComponent()
javax.swing.JComponent	getComponent()
boolean	getComponentFillAvailableSpace()
SequenceViewerExtension.ComponentLocation	getComponentLocation()
SequenceViewerExtension.ComponentLocation	getDefaultComponentLocation()
ExtendedPrintable	getExtendedPrintable()	Returns an ExtendedPrintable which describes how this extension should be printed.
abstract java.lang.String	getName()
java.util.List<SequenceViewerExtension.StatisticsSection>	getStatistics(SequenceViewerExtension.PropertyRetrieverAndEditor propertyRetriever, jebl.util.ProgressListener progressListener)	Generates one or more sections of statistics to be displayed in the statistics controls section.
java.util.List<GeneiousAction>	getToolbarActions()	Get a list of other actions associated with extension which will be displayed in the sequence viewer toolbar.
java.lang.String	getUniqueId()
void	setComponentLocation(SequenceViewerExtension.ComponentLocation location)	Sets the current location for this component.

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceViewerExtension

public SequenceViewerExtension()

Method Detail

getName

public abstract java.lang.String getName()

Returns:

a name describing this extension. This is used in the print dialog when selecting which part of the sequence viewer to print

getStatistics

public java.util.List<SequenceViewerExtension.StatisticsSection> getStatistics(SequenceViewerExtension.PropertyRetrieverAndEditor propertyRetriever,
                                                                               jebl.util.ProgressListener progressListener)

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

Rather than implementing a factory and extension classes to create statistics, plugins may wish to instead implement a SequenceViewerExtension.StatisticsFactory which is a simpler API for plugins which just provide statistics.

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

Since:

API 4.700 (Geneious 7.0.0)

getDefaultComponentLocation

public SequenceViewerExtension.ComponentLocation getDefaultComponentLocation()

Returns:

the default location the component returned from createComponent() will be displayed at. The user can choose to customize the location if addComponentPositionActions or addComponentPositionPopInOrOutAction is used.

getComponentFillAvailableSpace

public boolean getComponentFillAvailableSpace()

Returns:

true if the component returned from getComponent() should expand to fill all available space

getComponentLocation

public final SequenceViewerExtension.ComponentLocation getComponentLocation()

Returns:

the location for the component returned from createComponent() will be displayed at. The user can choose to customize the location if addComponentPositionActions or addComponentPositionPopInOrOutAction is used. Alternatively the extension can create its own controls to manage this itself

addComponentLocationChangedListener

public void addComponentLocationChangedListener(org.virion.jam.util.SimpleListener listener)

Adds a listener to be notified when the value returned from getComponentLocation() changes

Parameters:

listener - the listener to be notified

setComponentLocation

public void setComponentLocation(SequenceViewerExtension.ComponentLocation location)

Sets the current location for this component. The sequence viewer automatically calls this to restore the state the user last set.

Parameters:

location - the current location for this component.

addComponentPositionActions

public void addComponentPositionActions(GeneiousActionToolbar toolbar,
                                        SequenceViewerExtension.ComponentLocation... locations)

Adds little buttons to a toolbar to control the location (see getComponentLocation()) of the component (see getComponent()) in the sequence viewer. Consider using addComponentPositionPopInOrOutAction instead if you want your component to have only 2 possible locations.

Parameters:

toolbar - the toolbar to add buttons to

locations - possible locations for this component.

See Also:

addComponentPositionPopInOrOutAction(com.biomatters.geneious.publicapi.components.GeneiousActionToolbar, com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.ComponentLocation, com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.ComponentLocation)

addComponentPositionPopInOrOutAction

public void addComponentPositionPopInOrOutAction(GeneiousActionToolbar toolbar,
                                                 SequenceViewerExtension.ComponentLocation inLocation,
                                                 SequenceViewerExtension.ComponentLocation outLocation)

Adds a little button to the toolbar to control the location (see getComponentLocation()) of the component (see getComponent()) in the sequence viewer.

Parameters:

toolbar - the toolbar to add buttons to

inLocation - the location of this component when it is popped in. Either SequenceViewerExtension.ComponentLocation.AnnotationControls or SequenceViewerExtension.ComponentLocation.StatisticsControls

outLocation - the location of this component with it is popped out. Either SequenceViewerExtension.ComponentLocation.AdjacentToControls or SequenceViewerExtension.ComponentLocation.BelowSequenceViewer

Since:

API 4.61 (Geneious 5.6.1)

See Also:

addComponentPositionActions(com.biomatters.geneious.publicapi.components.GeneiousActionToolbar, com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.ComponentLocation...)

getToolbarActions

public java.util.List<GeneiousAction> getToolbarActions()

Get a list of other actions associated with extension which will be displayed in the sequence viewer toolbar. The toolbar buttons will be ordered according to their toolbar positions which can be set using GeneiousActionOptions.setToolbarPosition(double)

The default implementation returns an empty list.

Returns:

actions list. may be null or empty.

Since:

API 4.600 (Geneious 6.0.0)

See Also:

ActionProvider.getOtherActions()

getUniqueId

public java.lang.String getUniqueId()

Returns:

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

createComponent

protected javax.swing.JComponent createComponent()

Returns:

the component displayed in the sequence viewer at the location returned from getComponentLocation(). May be null for no component.

getComponent

public final javax.swing.JComponent getComponent()

Returns:

the component returned from createComponent(), caching it so that createComponent() is only called once.

getExtendedPrintable

public ExtendedPrintable getExtendedPrintable()

Returns an ExtendedPrintable which describes how this extension should be printed. The default implementation wraps the result of getComponent() in an ExtendedPrintable using ExtendedPrintable.Factory.createExtendedPrintable(javax.swing.JComponent)

Returns:

an ExtendedPrintable which describes how this extension should be printed or null if this extension is not suitable for printing.