Package org.biojava.bio.search
Interface SeqSimilaritySearchSubHit
- All Superinterfaces:
Annotatable
,Changeable
- All Known Implementing Classes:
SequenceDBSearchSubHit
,SimpleSeqSimilaritySearchSubHit
Objects of this type represent one particular sub-hit (one concrete
sequence stretch within a sequence and associated information) from
a sequence similarity search hit.
- Author:
- Gerald Loeffler, Keith James
-
Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic final class
ByScoreComparator
comparesSeqSimilaritySearchSubHit
s by their score.static final class
BySubjectStartComparator
comparesSeqSimilaritySearchSubHit
s by their start position on the subject sequence.Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final SeqSimilaritySearchSubHit.ByScoreComparator
byScore
contains aSeqSimilaritySearchSubHit
comparator which compares by the score of the sub-hit.static final SeqSimilaritySearchSubHit.BySubjectStartComparator
bySubjectStart
contains aSeqSimilaritySearchSubHit
comparator which compares by the start position of the sub-hit on the subject sequence.static final String
This object is used as the label for the query sequence in the alignment of the query sequence with this sub-hit sequence.Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
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Method Summary
Modifier and TypeMethodDescriptionReturn an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence.double
Return the E-value of this sub-hit.double
Return the P-value of this sub-hit.int
Return the end position of the sub-hit in the query sequence.int
Return the start position of the sub-hit in the query sequence.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
Return the start position of the sub-hit in the subject sequence.int
Return the start position of the 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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QUERY_LABEL
This object is used as the label for the query sequence in the alignment of the query sequence with this sub-hit sequence.- See Also:
-
byScore
byScore
contains aSeqSimilaritySearchSubHit
comparator which compares by the score of the sub-hit. -
bySubjectStart
bySubjectStart
contains aSeqSimilaritySearchSubHit
comparator which compares by the start position of the sub-hit on the subject sequence.
-
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Method Details
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getScore
double getScore()Return the score of this sub-hit in the units defined by the search algorithm.- 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
double getPValue()Return the P-value of this sub-hit.- 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
double getEValue()Return the E-value of this sub-hit.- 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
int getQueryStart()Return the start position of the sub-hit in the query sequence.- Returns:
- an
int
.
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getQueryEnd
int getQueryEnd()Return the end position of the sub-hit in the query sequence.- Returns:
- an
int
.
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getQueryStrand
Return the strand of the sub-hit with respect to the query sequence. This may be null for protein sequences.- Returns:
- a
Strand
.
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getSubjectStart
int getSubjectStart()Return the start position of the sub-hit in the subject sequence.- Returns:
- an
int
.
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getSubjectEnd
int getSubjectEnd()Return the start position of the 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. This may be null for protein sequences.- Returns:
- a
Strand
.
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getAlignment
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.- Returns:
- the alignment of the query sequence against this hit sequence.
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