Package com.biomatters.geneious.publicapi.plugin

Class SequenceViewerExtension.SequenceAnnotationWrapper

java.lang.Object

com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.SequenceAnnotationWrapper

Enclosing class:

SequenceViewerExtension

public abstract static class SequenceViewerExtension.SequenceAnnotationWrapper
extends Object

Wraps a SequenceAnnotation and provides extra information about the location (sequence, track) of the annotation. Plugins should not extend this class. Only the sequence viewer should extend it and it will provide implementations to sequence viewer extensions.

For test cases, plugins may wish to use PropertyRetrieverAndEditor.forSequences or PropertyRetrieverAndEditor.forAlignment to obtain a PropertyRetrieverAndEditor, and call PropertyRetrieverAndEditor.getVisibleAnnotations to obtain SequenceAnnotationWrappers.

Constructor Summary

Constructors

Constructor	Description
SequenceAnnotationWrapper()

Method Summary

Modifier and Type	Method	Description
static SequenceViewerExtension.SequenceAnnotationWrapper	forAnnotation(SequenceAnnotation annotation, int sequenceIndex, int trackIndex, boolean isSelected)	Wraps a SequenceAnnotation and provides extra information about the location (sequence, track) of the annotation.
abstract SequenceAnnotationInterval	getInterval(int intervalIndex)
abstract List<SequenceAnnotationInterval>	getIntervals()
abstract int	getNumberOfIntervals()
abstract List<SequenceAnnotationQualifier>	getQualifiers()
String	getQualifierValue(String name)
abstract SequenceAnnotation	getSequenceAnnotation()
abstract int	getSequenceIndex()
abstract int	getTrackIndex()
abstract String	getType()
abstract boolean	isSelected()

Methods inherited from class java.lang.Object

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

Constructor Details

SequenceAnnotationWrapper

public SequenceAnnotationWrapper()

Method Details

getSequenceAnnotation

public abstract SequenceAnnotation getSequenceAnnotation()

Returns:

the annotation wrapped by this wrapper

getSequenceIndex

public abstract int getSequenceIndex()

Returns:

the 0-based index of the sequence this annotation is on. May be -1 for consensus annotations.

isSelected

public abstract boolean isSelected()

Returns:

true if this annotation is selected

getTrackIndex

public abstract int getTrackIndex()

Returns:

the index of the track (if any) this annotation is on. -1 for no track. This index can be used with SequenceViewerExtension.PropertyRetrieverAndEditor.getTrackName(int, int)

getQualifiers

public abstract List<SequenceAnnotationQualifier> getQualifiers()

Returns:

the annotation qualifiers. Equivalent to getSequenceAnnotation().getQualifiers() but more efficient

getIntervals

public abstract List<SequenceAnnotationInterval> getIntervals()

Returns:

the annotation intervals. Equivalent to getSequenceAnnotation().getIntervals() but more efficient

getNumberOfIntervals

public abstract int getNumberOfIntervals()

Returns:

the number of annotation intervals. Equivalent to getSequenceAnnotation().getNumberOfIntervals() but more efficient

Since:

API 4.810 (Geneious 8.1.0)

getInterval

public abstract SequenceAnnotationInterval getInterval(int intervalIndex)

Returns:

one of the annotation intervals. Equivalent to getSequenceAnnotation().getInterval(...)} but more efficient

Since:

API 4.810 (Geneious 8.1.0)

getType

public abstract String getType()

Returns:

the annotation type of this annotation. Equivalent to getSequenceAnnotation().getType() but more efficient

getQualifierValue

public String getQualifierValue(String name)

Returns:

the value of one qualifier. Equivalent to getSequenceAnnotation().getQualifierValue(...)} but more efficient

Since:

API 4.900 (Geneious 9.0.0)

forAnnotation

public static SequenceViewerExtension.SequenceAnnotationWrapper forAnnotation(SequenceAnnotation annotation,
 int sequenceIndex,
 int trackIndex,
 boolean isSelected)

Wraps a SequenceAnnotation and provides extra information about the location (sequence, track) of the annotation.

Parameters:

annotation - the annotation to wrap.

sequenceIndex - the 0-based index of the sequence this annotation is on. May be -1 for consensus annotations.

trackIndex - the 0-based index of the track. May be -1 for no track.

isSelected - true if this annotation is selected.

Returns:

the wrapped SequenceAnnotation

Since:

API 4.900 (Geneious 9.0.0)