Package org.biojava.bio.search
Interface SeqSimilaritySearchHit
- All Superinterfaces:
Annotatable
,Changeable
- All Known Implementing Classes:
SequenceDBSearchHit
,SimpleSeqSimilaritySearchHit
Objects of this type represent one particular hit (sequence and
associated information) from a sequence similarity search.
- Author:
- Gerald Loeffler, Keith James
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Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic final class
ByScoreComparator
comparesSeqSimilaritySearchHit
s by their score.static final class
BySubHitCountComparator
comparesSeqSimilaritySearchHit
s by their number of sub-hits.Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final SeqSimilaritySearchHit.ByScoreComparator
byScore
contains aSeqSimilaritySearchHit
comparator which compares by their score.static final SeqSimilaritySearchHit.BySubHitCountComparator
bySubHitCount
contains aSeqSimilaritySearchHit
comparator which compares by their number of sub-hits.Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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Method Summary
Modifier and TypeMethodDescriptiondouble
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.Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Field Details
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byScore
byScore
contains aSeqSimilaritySearchHit
comparator which compares by their score. -
bySubHitCount
bySubHitCount
contains aSeqSimilaritySearchHit
comparator which compares by their number of sub-hits.
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Method Details
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getScore
double getScore()Return the overall score of this hit in the units defined by the search algorithm.- 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
double getPValue()Return the overall P-value of this hit.- 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
double getEValue()Return the overall E-value of this hit.- 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
int getQueryStart()Return the start position of the first sub-hit in the query sequence.- Returns:
- an
int
.
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getQueryEnd
int getQueryEnd()Return the end position of the last sub-hit in the query sequence.- Returns:
- an
int
.
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getQueryStrand
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.- Returns:
- a
Strand
.
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getSubjectStart
int getSubjectStart()Return the start position of the first sub-hit in the subject sequence.- Returns:
- an
int
.
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getSubjectEnd
int getSubjectEnd()Return the end position of the last sub-hit in the subject sequence.- Returns:
- an
int
.
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getSubjectStrand
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.- Returns:
- a
Strand
.
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getSubjectID
The sequence identifier of this hit within the sequence database against which the search was performed.- 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
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.- 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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