Package org.biojava.bio.search
Class SequenceDBSearchSubHit
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.search.SequenceDBSearchSubHit
- All Implemented Interfaces:
Annotatable
,SeqSimilaritySearchSubHit
,Changeable
Deprecated.
SimpleSeqSimilaritySearchSubHit has been made
Annotatable and is now functionally identical.
SequenceDBSearchSubHit
objects represent sub-hits
which make up a hit. In the case of Blast these correspond to
HSPs.
- Since:
- 1.1
- 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.search.SeqSimilaritySearchSubHit
SeqSimilaritySearchSubHit.ByScoreComparator, SeqSimilaritySearchSubHit.BySubjectStartComparator
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Field Summary
FieldsFields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
Fields inherited from interface org.biojava.bio.search.SeqSimilaritySearchSubHit
byScore, bySubjectStart, QUERY_LABEL
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Constructor Summary
ConstructorsConstructorDescriptionSequenceDBSearchSubHit
(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, Alignment alignment, Annotation annotation) Deprecated.Creates a newSequenceDBSearchSubHit
object. -
Method Summary
Modifier and TypeMethodDescriptionboolean
Deprecated.Deprecated.Return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence.Deprecated.Should return the associated annotation object.protected ChangeSupport
Deprecated.Called to retrieve the ChangeSupport for this object.double
Deprecated.Return the E-value of this sub-hit.double
Deprecated.Return the P-value of this sub-hit.int
Deprecated.Return the end position of the sub-hit in the query sequence.int
Deprecated.Return the start position of the sub-hit in the query sequence.Deprecated.Return the strand of the sub-hit with respect to the query sequence.double
getScore()
Deprecated.Return the score of this sub-hit in the units defined by the search algorithm.int
Deprecated.Return the start position of the sub-hit in the subject sequence.int
Deprecated.Return the start position of the sub-hit in the subject sequence.Deprecated.Return the strand of the sub-hit with respect to the subject sequence.int
hashCode()
Deprecated.toString()
Deprecated.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
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Field Details
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annotationForwarder
Deprecated.
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Constructor Details
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SequenceDBSearchSubHit
public SequenceDBSearchSubHit(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, Alignment alignment, Annotation annotation) Deprecated.Creates a newSequenceDBSearchSubHit
object.- Parameters:
score
- adouble
value; the score of the subhit, which may not be NaN.eValue
- adouble
the E-value of the subhit, which may be NaN.pValue
- adouble
value; the P-value of the hit, which may be NaN.queryStart
- anint
value indicating the start coordinate of the hit on the query sequence.queryEnd
- anint
value indicating the end coordinate of the hit on the query sequence.queryStrand
- aStrand
object indicating the strand of the hit with respect to the query sequence, which may be null for protein similarities.subjectStart
- anint
value indicating the start coordinate of the hit on the subject sequence.subjectEnd
- anint
value indicating the end coordinate of the hit on the query sequence.subjectStrand
- aStrand
object indicating the strand of the hit with respect to the query sequence, which may be null for protein similarities.alignment
- anAlignment
object containing the alignment described by the subhit region, which may not be null.annotation
- anAnnotation
object, which may not be null.
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Method Details
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getScore
Deprecated.Description copied from interface:SeqSimilaritySearchSubHit
Return the score of this sub-hit in the units defined by the search algorithm.- Specified by:
getScore
in interfaceSeqSimilaritySearchSubHit
- Returns:
- the score of this sub-hit. This is a mandatory piece of information and hence may not be NaN.
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getPValue
Deprecated.Description copied from interface:SeqSimilaritySearchSubHit
Return the P-value of this sub-hit.- Specified by:
getPValue
in interfaceSeqSimilaritySearchSubHit
- 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.
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getEValue
Deprecated.Description copied from interface:SeqSimilaritySearchSubHit
Return the E-value of this sub-hit.- Specified by:
getEValue
in interfaceSeqSimilaritySearchSubHit
- 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.
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getQueryStart
Deprecated.Description copied from interface:SeqSimilaritySearchSubHit
Return the start position of the sub-hit in the query sequence.- Specified by:
getQueryStart
in interfaceSeqSimilaritySearchSubHit
- Returns:
- an
int
.
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getQueryEnd
Deprecated.Description copied from interface:SeqSimilaritySearchSubHit
Return the end position of the sub-hit in the query sequence.- Specified by:
getQueryEnd
in interfaceSeqSimilaritySearchSubHit
- Returns:
- an
int
.
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getQueryStrand
Deprecated.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 interfaceSeqSimilaritySearchSubHit
- Returns:
- a
Strand
.
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getSubjectStart
Deprecated.Description copied from interface:SeqSimilaritySearchSubHit
Return the start position of the sub-hit in the subject sequence.- Specified by:
getSubjectStart
in interfaceSeqSimilaritySearchSubHit
- Returns:
- an
int
.
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getSubjectEnd
Deprecated.Description copied from interface:SeqSimilaritySearchSubHit
Return the start position of the sub-hit in the subject sequence.- Specified by:
getSubjectEnd
in interfaceSeqSimilaritySearchSubHit
- Returns:
- an
int
.
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getSubjectStrand
Deprecated.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 interfaceSeqSimilaritySearchSubHit
- Returns:
- a
Strand
.
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getAlignment
Deprecated.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 interfaceSeqSimilaritySearchSubHit
- Returns:
- the alignment of the query sequence against this hit sequence.
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getAnnotation
Deprecated.Description copied from interface:Annotatable
Should return the associated annotation object.- Specified by:
getAnnotation
in interfaceAnnotatable
- Returns:
- an Annotation object, never null
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equals
Deprecated. -
hashCode
Deprecated. -
toString
Deprecated. -
getChangeSupport
Deprecated.Description copied from class:AbstractChangeable
Called to retrieve the ChangeSupport for this object.Your implementation of this method should have the following structure:
It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register invalid input: '&' unregister the forwarder in the code that does the ChangeEvent handling in setter methods.ChangeSupport cs = super.getChangeSupport(ct); if(someForwarder == null invalid input: '&'invalid input: '&' ct.isMatching(SomeInterface.SomeChangeType)) { someForwarder = new ChangeForwarder(... this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange); } return cs;
- Overrides:
getChangeSupport
in classAbstractChangeable
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