Package org.biojava.bio.seq.impl

Class SimpleSimilarityPairFeature

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.impl.SimpleFeature

org.biojava.bio.seq.impl.SimpleStrandedFeature

org.biojava.bio.seq.impl.SimpleSimilarityPairFeature

All Implemented Interfaces:

Serializable, Annotatable, Feature, FeatureHolder, SimilarityPairFeature, RealizingFeatureHolder, StrandedFeature, Changeable

public class SimpleSimilarityPairFeature
extends SimpleStrandedFeature
implements SimilarityPairFeature

SimpleSimilarityPairFeature represents a similarity between a query sequence and a subject sequence as produced by a search program.

Since:

1.2

Author:

Keith James

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Nested classes/interfaces inherited from interface org.biojava.bio.seq.Feature

Feature.ByLocationComparator, Feature.Template

Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder

FeatureHolder.EmptyFeatureHolder

Nested classes/interfaces inherited from interface org.biojava.bio.seq.homol.SimilarityPairFeature

SimilarityPairFeature.EmptyPairwiseAlignment, SimilarityPairFeature.Template

Nested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature

StrandedFeature.Strand, StrandedFeature.Template

Field Summary

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Fields inherited from interface org.biojava.bio.seq.Feature

byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERM

Fields inherited from interface org.biojava.bio.seq.FeatureHolder

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Fields inherited from interface org.biojava.bio.seq.homol.SimilarityPairFeature

EMPTY_PAIRWISE, QUERY_LABEL, SIBLING, SUBJECT_LABEL

Fields inherited from interface org.biojava.bio.seq.StrandedFeature

NEGATIVE, POSITIVE, STRAND, UNKNOWN

Constructor Summary

Constructors

Constructor	Description
SimpleSimilarityPairFeature(Sequence sourceSeq, FeatureHolder parent, SimilarityPairFeature.Template template)	Creates a new SimpleSimilarityPairFeature.

Method Summary

Modifier and Type	Method	Description
protected void	fillTemplate(SimilarityPairFeature.Template ft)
Alignment	getAlignment()	getAlignment returns the alignment between the two features.
double	getScore()	getScore returns the alignment score.
SimilarityPairFeature	getSibling()	getSibling returns the sibling feature of the pair.
Feature.Template	makeTemplate()	Create a new Template that could be used to generate a feature identical to this one.
void	setSibling(SimilarityPairFeature sibling)	setSibling sets the sibling feature of the pair.
String	toString()

Methods inherited from class org.biojava.bio.seq.impl.SimpleStrandedFeature

fillTemplate, getStrand, getSymbols, setStrand

Methods inherited from class org.biojava.bio.seq.impl.SimpleFeature

containsFeature, countFeatures, createFeature, equals, featureHolderAllocated, features, fillTemplate, filter, filter, getAnnotation, getChangeSupport, getFeatureHolder, getLocation, getParent, getSchema, getSequence, getSource, getSourceTerm, getType, getTypeTerm, hashCode, realizeFeature, removeFeature, setLocation, setSource, setSourceTerm, setType, setTypeTerm

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.seq.Feature

features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, setLocation, setSource, setSourceTerm, setType, setTypeTerm

Methods inherited from interface org.biojava.bio.seq.FeatureHolder

containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature

Methods inherited from interface org.biojava.bio.seq.StrandedFeature

getStrand, getSymbols, setStrand

Constructor Detail

SimpleSimilarityPairFeature

public SimpleSimilarityPairFeature(Sequence sourceSeq,
                                   FeatureHolder parent,
                                   SimilarityPairFeature.Template template)
                            throws IllegalAlphabetException

Creates a new SimpleSimilarityPairFeature.

Parameters:

sourceSeq - a Sequence.

parent - a FeatureHolder.

template - a SimilarityPairFeature.Template.

Throws:

IllegalAlphabetException

Method Detail

getSibling

public SimilarityPairFeature getSibling()

getSibling returns the sibling feature of the pair.

Specified by:

getSibling in interface SimilarityPairFeature

Returns:

a Feature.

setSibling

public void setSibling(SimilarityPairFeature sibling)
                throws ChangeVetoException

Description copied from interface: SimilarityPairFeature

setSibling sets the sibling feature of the pair. This is used to set the reciprocal SimilarityPairFeature as both cannot be set using the Template.

Specified by:

setSibling in interface SimilarityPairFeature

Throws:

ChangeVetoException

getAlignment

public Alignment getAlignment()

getAlignment returns the alignment between the two features.

Specified by:

getAlignment in interface SimilarityPairFeature

Returns:

an Alignment.

getScore

public double getScore()

getScore returns the alignment score.

Specified by:

getScore in interface SimilarityPairFeature

Returns:

a double.

makeTemplate

public Feature.Template makeTemplate()

Description copied from interface: Feature

Create a new Template that could be used to generate a feature identical to this one. The fields of the template can be edited without changing the feature.

Specified by:

makeTemplate in interface Feature

Overrides:

makeTemplate in class SimpleStrandedFeature

Returns:

a new Template that would make a feature like this one

fillTemplate

protected void fillTemplate(SimilarityPairFeature.Template ft)

toString

public String toString()

Overrides:

toString in class SimpleStrandedFeature