Package org.biojava.bio.search

Class SimpleSeqSimilaritySearchSubHit

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit

All Implemented Interfaces:

Annotatable, SeqSimilaritySearchSubHit, Changeable

public class SimpleSeqSimilaritySearchSubHit
extends AbstractChangeable
implements SeqSimilaritySearchSubHit

SimpleSeqSimilaritySearchSubHit objects represent sub-hits which make up a hit. In the case of Blast these correspond to HSPs.

Since:

1.1

Author:

Keith James, Gerald Loeffler

Nested Class Summary

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

Annotatable.AnnotationForwarder

Nested classes/interfaces inherited from interface org.biojava.bio.search.SeqSimilaritySearchSubHit

SeqSimilaritySearchSubHit.ByScoreComparator, SeqSimilaritySearchSubHit.BySubjectStartComparator

Field Summary

Fields

Modifier and Type	Field	Description
protected ChangeForwarder	annotationForwarder

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Fields inherited from interface org.biojava.bio.search.SeqSimilaritySearchSubHit

byScore, bySubjectStart, QUERY_LABEL

Constructor Summary

Constructors

Constructor	Description
SimpleSeqSimilaritySearchSubHit(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, Alignment alignment, Annotation annotation)	Creates a new SimpleSeqSimilaritySearchSubHit object.

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object other)
Alignment	getAlignment()	Return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence.
Annotation	getAnnotation()	getAnnotation returns the Annotation associated with this sub-hit.
protected ChangeSupport	getChangeSupport(ChangeType ct)	Called to retrieve the ChangeSupport for this object.
double	getEValue()	Return the E-value of this sub-hit.
double	getPValue()	Return the P-value of this sub-hit.
int	getQueryEnd()	Return the end position of the sub-hit in the query sequence.
int	getQueryStart()	Return the start position of the sub-hit in the query sequence.
StrandedFeature.Strand	getQueryStrand()	Return the strand of the sub-hit with respect to the query sequence.
double	getScore()	Return the score of this sub-hit in the units defined by the search algorithm.
int	getSubjectEnd()	Return the start position of the sub-hit in the subject sequence.
int	getSubjectStart()	Return the start position of the sub-hit in the subject sequence.
StrandedFeature.Strand	getSubjectStrand()	Return the strand of the sub-hit with respect to the subject sequence.
int	hashCode()
String	toString()

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.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

annotationForwarder

protected transient ChangeForwarder annotationForwarder

Constructor Detail

SimpleSeqSimilaritySearchSubHit

public SimpleSeqSimilaritySearchSubHit(double score,
                                       double eValue,
                                       double pValue,
                                       int queryStart,
                                       int queryEnd,
                                       StrandedFeature.Strand queryStrand,
                                       int subjectStart,
                                       int subjectEnd,
                                       StrandedFeature.Strand subjectStrand,
                                       Alignment alignment,
                                       Annotation annotation)

Creates a new SimpleSeqSimilaritySearchSubHit object.

Parameters:

queryStart - an int value indicating the start coordinate of the hit on the query sequence.

queryEnd - an int value indicating the end coordinate of the hit on the query sequence.

queryStrand - a Strand object indicating the strand of the hit with respect to the query sequence, which may be null for protein similarities.

subjectStart - an int value indicating the start coordinate of the hit on the subject sequence.

subjectEnd - an int value indicating the end coordinate of the hit on the query sequence.

subjectStrand - a Strand object indicating the strand of the hit with respect to the query sequence, which may be null for protein similarities.

score - a double value; the score of the subhit, which may not be NaN.

eValue - a double the E-value of the subhit, which may be NaN.

pValue - a double value; the P-value of the hit, which may be NaN.

alignment - an Alignment object containing the alignment described by the subhit region, which may not be null.

Method Detail

getScore

public double getScore()

Description copied from interface: SeqSimilaritySearchSubHit

Return the score of this sub-hit in the units defined by the search algorithm.

Specified by:

getScore in interface SeqSimilaritySearchSubHit

Returns:

the score of this sub-hit. This is a mandatory piece of information and hence may not be NaN.

getPValue

public double getPValue()

Description copied from interface: SeqSimilaritySearchSubHit

Return the P-value of this sub-hit.

Specified by:

getPValue in interface SeqSimilaritySearchSubHit

Returns:

the P-value of this sub-hit. This is an optional (but desired) piece of information and implementations of this interface may return NaN if a P-value is not available for this hit.

getEValue

public double getEValue()

Description copied from interface: SeqSimilaritySearchSubHit

Return the E-value of this sub-hit.

Specified by:

getEValue in interface SeqSimilaritySearchSubHit

Returns:

the E-value of this sub-hit. This is an optional (but desired) piece of information and implementations of this interface may return NaN if an E-value is not available for this hit.

getQueryStart

public int getQueryStart()

Description copied from interface: SeqSimilaritySearchSubHit

Return the start position of the sub-hit in the query sequence.

Specified by:

getQueryStart in interface SeqSimilaritySearchSubHit

Returns:

an int.

getQueryEnd

public int getQueryEnd()

Description copied from interface: SeqSimilaritySearchSubHit

Return the end position of the sub-hit in the query sequence.

Specified by:

getQueryEnd in interface SeqSimilaritySearchSubHit

Returns:

an int.

getQueryStrand

public StrandedFeature.Strand getQueryStrand()

Description copied from interface: SeqSimilaritySearchSubHit

Return the strand of the sub-hit with respect to the query sequence. This may be null for protein sequences.

Specified by:

getQueryStrand in interface SeqSimilaritySearchSubHit

Returns:

a Strand.

getSubjectStart

public int getSubjectStart()

Description copied from interface: SeqSimilaritySearchSubHit

Return the start position of the sub-hit in the subject sequence.

Specified by:

getSubjectStart in interface SeqSimilaritySearchSubHit

Returns:

an int.

getSubjectEnd

public int getSubjectEnd()

Description copied from interface: SeqSimilaritySearchSubHit

Return the start position of the sub-hit in the subject sequence.

Specified by:

getSubjectEnd in interface SeqSimilaritySearchSubHit

Returns:

an int.

getSubjectStrand

public StrandedFeature.Strand getSubjectStrand()

Description copied from interface: SeqSimilaritySearchSubHit

Return the strand of the sub-hit with respect to the subject sequence. This may be null for protein sequences.

Specified by:

getSubjectStrand in interface SeqSimilaritySearchSubHit

Returns:

a Strand.

getAlignment

public Alignment getAlignment()

Description copied from interface: SeqSimilaritySearchSubHit

Return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence. In this alignment, the query is identified by the label given by the static field QUERY_LABEL.

Specified by:

getAlignment in interface SeqSimilaritySearchSubHit

Returns:

the alignment of the query sequence against this hit sequence.

getAnnotation

public Annotation getAnnotation()

getAnnotation returns the Annotation associated with this sub-hit.

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation.

equals

public boolean equals(Object other)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object.

Your implementation of this method should have the following structure:

 ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
 

It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.

Overrides:

getChangeSupport in class AbstractChangeable