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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 | |
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 inherited from class org.biojava.bio.Annotatable |
Annotatable.AnnotationForwarder |
Field Summary | |
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 java.lang.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 |
ANNOTATION |
Method Summary | |
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 |
getAnnotation |
Methods inherited from interface org.biojava.utils.Changeable |
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Field Detail |
public static final java.lang.String QUERY_LABEL
public static final SeqSimilaritySearchSubHit.ByScoreComparator byScore
byScore
contains a
SeqSimilaritySearchSubHit
comparator which
compares by the score of the sub-hit.
public 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 |
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 Alignment getAlignment()
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