Class SimpleSeqSimilaritySearchHit
- All Implemented Interfaces:
Annotatable
,SeqSimilaritySearchHit
,Changeable
SimpleSeqSimilaritySearchHit
objects represent a
similarity search hit of a query sequence to a sequence referenced
in a SequenceDB object. The core data (score, E-value, P-value)
have accessors, while supplementary data are stored in the
Annotation object. Supplementary data are typically the more
loosely formatted details which vary from one search program to
another (and between versions of those programs).
It is up to the user to define the meaning of the hit's query/subject start/end/strand with respect to its constituent sub-hits. One approach could be:
- Hit query/subject start == start of first sub-hit
- Hit query/subject end == end of last sub-hit
- Hit strand == POSITIVE if all sub-hits have strand POSITIVE
- Hit strand == NEGATIVE if all sub-hits have strand NEGATIVE
- Hit strand == UNKNOWN if sub-hits have either mixed or any UNKNOWN strands
- Hit strand == null if the concept of strandedness is inappropriate for the sequence type i.e. for protein
- Since:
- 1.1
- Author:
- Keith James, Gerald Loeffler
- See Also:
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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.SeqSimilaritySearchHit
SeqSimilaritySearchHit.ByScoreComparator, SeqSimilaritySearchHit.BySubHitCountComparator
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Field Summary
FieldsFields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
Fields inherited from interface org.biojava.bio.search.SeqSimilaritySearchHit
byScore, bySubHitCount
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Constructor Summary
ConstructorsConstructorDescriptionSimpleSeqSimilaritySearchHit
(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, String subjectID, Annotation annotation, List subHits) Creates a newSimpleSeqSimilaritySearchHit
object. -
Method Summary
Modifier and TypeMethodDescriptionboolean
getAnnotation
returns the Annotation associated with this hit.protected ChangeSupport
Called to retrieve the ChangeSupport for this object.double
Return the overall E-value of this hit.double
Return the overall P-value of this hit.int
Return the end position of the last sub-hit in the query sequence.int
Return the start position of the first sub-hit in the query sequence.Return the strand of the hit with respect to the query sequence.double
getScore()
Return the overall score of this hit in the units defined by the search algorithm.Return all sub-hits for this sequence similarity search hit.int
Return the end position of the last sub-hit in the subject sequence.The sequence identifier of this hit within the sequence database against which the search was performed.int
Return the start position of the first sub-hit in the subject sequence.Return the strand of the sub-hit with respect to the subject sequence.int
hashCode()
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
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Field Details
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annotationForwarder
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Constructor Details
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SimpleSeqSimilaritySearchHit
public SimpleSeqSimilaritySearchHit(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, String subjectID, Annotation annotation, List subHits) Creates a newSimpleSeqSimilaritySearchHit
object.- Parameters:
score
- adouble
value; the score of the hit, which may not be NaN.eValue
- adouble
value; the E-value of the hit, which may be NaN.pValue
- adouble
value; the P-value of the hit, which may be NaN.queryStart
- the start of the first sub-hit on the query sequence.queryEnd
- the end of the last sub-hit on the query sequence.queryStrand
- the strand of the sub-hits on the query sequence, which may be null for protein similarities. If they are not all positive or all negative, then this should be the unknown strand.subjectStart
- the start of the first sub-hit on the subject sequence.subjectEnd
- the end of the last sub-hit on the subject sequence.subjectStrand
- the strand of the sub-hits on the subject sequence, which may be null for protein similarities. If they are not all positive or all negative, then this should be the unknown strand.subjectID
- aString
representing the ID in the SequenceDB of the sequence which was hit, which may not be null.annotation
- anAnnotation
object, which may not be null.subHits
- aList
object containing the subhits, which may not be null. They should be sorted in the order specified by the search program.
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Method Details
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getScore
Description copied from interface:SeqSimilaritySearchHit
Return the overall score of this hit in the units defined by the search algorithm.- Specified by:
getScore
in interfaceSeqSimilaritySearchHit
- Returns:
- the overall score of this hit. This is a mandatory piece of information and hence may not be NaN.
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getPValue
Description copied from interface:SeqSimilaritySearchHit
Return the overall P-value of this hit.- Specified by:
getPValue
in interfaceSeqSimilaritySearchHit
- Returns:
- the overall P-value of this 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
Description copied from interface:SeqSimilaritySearchHit
Return the overall E-value of this hit.- Specified by:
getEValue
in interfaceSeqSimilaritySearchHit
- Returns:
- the overall E-value of this 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
Description copied from interface:SeqSimilaritySearchHit
Return the start position of the first sub-hit in the query sequence.- Specified by:
getQueryStart
in interfaceSeqSimilaritySearchHit
- Returns:
- an
int
.
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getQueryEnd
Description copied from interface:SeqSimilaritySearchHit
Return the end position of the last sub-hit in the query sequence.- Specified by:
getQueryEnd
in interfaceSeqSimilaritySearchHit
- Returns:
- an
int
.
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getQueryStrand
Description copied from interface:SeqSimilaritySearchHit
Return the strand of the hit with respect to the query sequence. If the sub-hits are not all on the same strand this should return the unknown strand. This may be null for protein sequences.- Specified by:
getQueryStrand
in interfaceSeqSimilaritySearchHit
- Returns:
- a
Strand
.
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getSubjectStart
Description copied from interface:SeqSimilaritySearchHit
Return the start position of the first sub-hit in the subject sequence.- Specified by:
getSubjectStart
in interfaceSeqSimilaritySearchHit
- Returns:
- an
int
.
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getSubjectEnd
Description copied from interface:SeqSimilaritySearchHit
Return the end position of the last sub-hit in the subject sequence.- Specified by:
getSubjectEnd
in interfaceSeqSimilaritySearchHit
- Returns:
- an
int
.
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getSubjectStrand
Description copied from interface:SeqSimilaritySearchHit
Return the strand of the sub-hit with respect to the subject sequence. If the sub-hits are not all on the same strand this should return the unknown strand. This may be null for protein sequences.- Specified by:
getSubjectStrand
in interfaceSeqSimilaritySearchHit
- Returns:
- a
Strand
.
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getSubjectID
Description copied from interface:SeqSimilaritySearchHit
The sequence identifier of this hit within the sequence database against which the search was performed.- Specified by:
getSubjectID
in interfaceSeqSimilaritySearchHit
- Returns:
- the (unique) sequence identifier for this hit, valid within the sequence database against which this search was performed. Never returns null.
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getSubHits
Description copied from interface:SeqSimilaritySearchHit
Return all sub-hits for this sequence similarity search hit. The sub-hits contain concrete alignments (and scores) for sequence stretches from the sequence of this hit. The sub-hits in the list returned by this method are sorted from best to worst.- Specified by:
getSubHits
in interfaceSeqSimilaritySearchHit
- Returns:
- a List of SeqSimilaritySearchSubHit objects containing all sub-hits for this hit. Never returns null and the List is guaranteed to contain at least one entry.
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getAnnotation
getAnnotation
returns the Annotation associated with this hit.- Specified by:
getAnnotation
in interfaceAnnotatable
- Returns:
- an
Annotation
.
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equals
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hashCode
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toString
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getChangeSupport
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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