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Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.
Nested Class Summary | |
static class |
SeqSimilaritySearchHit.ByScoreComparator
ByScoreComparator compares
SeqSimilaritySearchHit s by their score. |
static class |
SeqSimilaritySearchHit.BySubHitCountComparator
BySubHitCountComparator compares
SeqSimilaritySearchHit s by their number of
sub-hits. |
Nested classes inherited from class org.biojava.bio.Annotatable |
Annotatable.AnnotationForwarder |
Field Summary | |
static SeqSimilaritySearchHit.ByScoreComparator |
byScore
byScore contains a
SeqSimilaritySearchHit comparator which
compares by their score. |
static SeqSimilaritySearchHit.BySubHitCountComparator |
bySubHitCount
bySubHitCount contains a
SeqSimilaritySearchHit comparator which
compares by their number of sub-hits. |
Fields inherited from interface org.biojava.bio.Annotatable |
ANNOTATION |
Method Summary | |
double |
getEValue()
Return the overall E-value of this hit. |
double |
getPValue()
Return the overall P-value of this hit. |
int |
getQueryEnd()
Return the end position of the last sub-hit in the query sequence. |
int |
getQueryStart()
Return the start position of the first sub-hit in the query sequence. |
StrandedFeature.Strand |
getQueryStrand()
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. |
java.util.List |
getSubHits()
Return all sub-hits for this sequence similarity search hit. |
int |
getSubjectEnd()
Return the end position of the last sub-hit in the subject sequence. |
java.lang.String |
getSubjectID()
The sequence identifier of this hit within the sequence database against which the search was performed. |
int |
getSubjectStart()
Return the start position of the first 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 |
getAnnotation |
Methods inherited from interface org.biojava.utils.Changeable |
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Field Detail |
public static final SeqSimilaritySearchHit.ByScoreComparator byScore
byScore
contains a
SeqSimilaritySearchHit
comparator which
compares by their score.
public static final SeqSimilaritySearchHit.BySubHitCountComparator bySubHitCount
bySubHitCount
contains a
SeqSimilaritySearchHit
comparator which
compares by their number of sub-hits.
Method Detail |
public double getScore()
public double getPValue()
public double getEValue()
public int getQueryStart()
int
.public int getQueryEnd()
int
.public StrandedFeature.Strand getQueryStrand()
Strand
.public int getSubjectStart()
int
.public int getSubjectEnd()
int
.public StrandedFeature.Strand getSubjectStrand()
Strand
.public java.lang.String getSubjectID()
public java.util.List getSubHits()
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