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:
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarderNested classes/interfaces inherited from interface org.biojava.bio.seq.Feature
Feature.ByLocationComparator, Feature.TemplateNested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolderNested classes/interfaces inherited from interface org.biojava.bio.seq.homol.SimilarityPairFeature
SimilarityPairFeature.EmptyPairwiseAlignment, SimilarityPairFeature.TemplateNested classes/interfaces inherited from interface org.biojava.bio.seq.StrandedFeature
StrandedFeature.Strand, StrandedFeature.Template -
Field Summary
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATIONFields inherited from interface org.biojava.bio.seq.Feature
byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERMFields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMAFields inherited from interface org.biojava.bio.seq.homol.SimilarityPairFeature
EMPTY_PAIRWISE, QUERY_LABEL, SIBLING, SUBJECT_LABELFields inherited from interface org.biojava.bio.seq.StrandedFeature
NEGATIVE, POSITIVE, STRAND, UNKNOWN -
Constructor Summary
ConstructorsConstructorDescriptionSimpleSimilarityPairFeature(Sequence sourceSeq, FeatureHolder parent, SimilarityPairFeature.Template template) Creates a newSimpleSimilarityPairFeature. -
Method Summary
Modifier and TypeMethodDescriptionprotected voidgetAlignmentreturns the alignment between the two features.doublegetScore()getScorereturns the alignment score.getSiblingreturns the sibling feature of the pair.Create a new Template that could be used to generate a feature identical to this one.voidsetSibling(SimilarityPairFeature sibling) setSiblingsets the sibling feature of the pair.toString()Methods inherited from class org.biojava.bio.seq.impl.SimpleStrandedFeature
fillTemplate, getStrand, getSymbols, setStrandMethods 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, setTypeTermMethods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListenerMethods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, waitMethods inherited from interface org.biojava.bio.Annotatable
getAnnotationMethods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListenerMethods inherited from interface org.biojava.bio.seq.Feature
features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, setLocation, setSource, setSourceTerm, setType, setTypeTermMethods inherited from interface org.biojava.bio.seq.FeatureHolder
containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeatureMethods inherited from interface org.biojava.bio.seq.StrandedFeature
getStrand, getSymbols, setStrand
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Constructor Details
-
SimpleSimilarityPairFeature
public SimpleSimilarityPairFeature(Sequence sourceSeq, FeatureHolder parent, SimilarityPairFeature.Template template) throws IllegalAlphabetException Creates a newSimpleSimilarityPairFeature.- Parameters:
sourceSeq- aSequence.parent- aFeatureHolder.template- aSimilarityPairFeature.Template.- Throws:
IllegalAlphabetException
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Method Details
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getSibling
getSiblingreturns the sibling feature of the pair.- Specified by:
getSiblingin interfaceSimilarityPairFeature- Returns:
- a
Feature.
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setSibling
Description copied from interface:SimilarityPairFeaturesetSiblingsets the sibling feature of the pair. This is used to set the reciprocalSimilarityPairFeatureas both cannot be set using theTemplate.- Specified by:
setSiblingin interfaceSimilarityPairFeature- Throws:
ChangeVetoException
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getAlignment
getAlignmentreturns the alignment between the two features.- Specified by:
getAlignmentin interfaceSimilarityPairFeature- Returns:
- an
Alignment.
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getScore
getScorereturns the alignment score.- Specified by:
getScorein interfaceSimilarityPairFeature- Returns:
- a
double.
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makeTemplate
Description copied from interface:FeatureCreate 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:
makeTemplatein interfaceFeature- Overrides:
makeTemplatein classSimpleStrandedFeature- Returns:
- a new Template that would make a feature like this one
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fillTemplate
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toString
- Overrides:
toStringin classSimpleStrandedFeature
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