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:
-
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
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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
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Constructor Summary
ConstructorsConstructorDescriptionSimpleSimilarityPairFeature
(Sequence sourceSeq, FeatureHolder parent, SimilarityPairFeature.Template template) Creates a newSimpleSimilarityPairFeature
. -
Method Summary
Modifier and TypeMethodDescriptionprotected void
getAlignment
returns the alignment between the two features.double
getScore()
getScore
returns the alignment score.getSibling
returns the sibling feature of the pair.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.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
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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
-
-
Method Details
-
getSibling
getSibling
returns the sibling feature of the pair.- Specified by:
getSibling
in interfaceSimilarityPairFeature
- Returns:
- a
Feature
.
-
setSibling
Description copied from interface:SimilarityPairFeature
setSibling
sets the sibling feature of the pair. This is used to set the reciprocalSimilarityPairFeature
as both cannot be set using theTemplate
.- Specified by:
setSibling
in interfaceSimilarityPairFeature
- Throws:
ChangeVetoException
-
getAlignment
getAlignment
returns the alignment between the two features.- Specified by:
getAlignment
in interfaceSimilarityPairFeature
- Returns:
- an
Alignment
.
-
getScore
getScore
returns the alignment score.- Specified by:
getScore
in interfaceSimilarityPairFeature
- Returns:
- a
double
.
-
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 interfaceFeature
- Overrides:
makeTemplate
in classSimpleStrandedFeature
- Returns:
- a new Template that would make a feature like this one
-
fillTemplate
-
toString
- Overrides:
toString
in classSimpleStrandedFeature
-