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
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 interface org.biojava.bio.seq.Feature |
features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, setLocation, setSource, setSourceTerm, setType, setTypeTerm |
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
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