public interface SeqSimilaritySearchSubHit extends Annotatable
Modifier and Type | Interface and Description |
---|---|
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. |
Annotatable.AnnotationForwarder
Modifier and Type | Field and Description |
---|---|
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.
|
ANNOTATION
Modifier and Type | Method and Description |
---|---|
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.
|
getAnnotation
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
static final java.lang.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.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()