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public interface SeqSimilaritySearchSubHit
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.
Nested Class Summary | |
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static class |
SeqSimilaritySearchSubHit.ByScoreComparator
ByScoreComparator compares
SeqSimilaritySearchSubHit s by their score. |
static class |
SeqSimilaritySearchSubHit.BySubjectStartComparator
BySubjectStartComparator compares
SeqSimilaritySearchSubHit s by their start position
on the subject sequence. |
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable |
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Annotatable.AnnotationForwarder |
Field Summary | |
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static SeqSimilaritySearchSubHit.ByScoreComparator |
byScore
byScore contains a
SeqSimilaritySearchSubHit comparator which
compares by the score of the sub-hit. |
static SeqSimilaritySearchSubHit.BySubjectStartComparator |
bySubjectStart
bySubjectStart contains a
SeqSimilaritySearchSubHit comparator which
compares by the start position of the sub-hit on the subject
sequence. |
static String |
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. |
Fields inherited from interface org.biojava.bio.Annotatable |
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ANNOTATION |
Method Summary | |
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Alignment |
getAlignment()
Return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence. |
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. |
Methods inherited from interface org.biojava.bio.Annotatable |
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getAnnotation |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Field Detail |
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static final String QUERY_LABEL
static final SeqSimilaritySearchSubHit.ByScoreComparator byScore
byScore
contains a
SeqSimilaritySearchSubHit
comparator which
compares by the score of the sub-hit.
static final SeqSimilaritySearchSubHit.BySubjectStartComparator bySubjectStart
bySubjectStart
contains a
SeqSimilaritySearchSubHit
comparator which
compares by the start position of the sub-hit on the subject
sequence.
Method Detail |
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double getScore()
double getPValue()
double getEValue()
int getQueryStart()
int
.int getQueryEnd()
int
.StrandedFeature.Strand getQueryStrand()
Strand
.int getSubjectStart()
int
.int getSubjectEnd()
int
.StrandedFeature.Strand getSubjectStrand()
Strand
.Alignment getAlignment()
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