org.biojava.bio.search
Interface SeqSimilaritySearchSubHit

All Superinterfaces:

Annotatable, Changeable

All Known Implementing Classes:

SequenceDBSearchSubHit, SimpleSeqSimilaritySearchSubHit

public interface SeqSimilaritySearchSubHit

extends Annotatable

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

static class	SeqSimilaritySearchSubHit.ByScoreComparator ByScoreComparator compares SeqSimilaritySearchSubHits by their score.
static class	SeqSimilaritySearchSubHit.BySubjectStartComparator BySubjectStartComparator compares SeqSimilaritySearchSubHits 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

QUERY_LABEL

public static final 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.

See Also:

Constant Field Values

byScore

public static final SeqSimilaritySearchSubHit.ByScoreComparator byScore

byScore contains a SeqSimilaritySearchSubHit comparator which compares by the score of the sub-hit.

bySubjectStart

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

getScore

public 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.

getPValue

public 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.

getEValue

public 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.

getQueryStart

public int getQueryStart()

Return the start position of the sub-hit in the query sequence.

Returns:

an int.

getQueryEnd

public int getQueryEnd()

Return the end position of the sub-hit in the query sequence.

Returns:

an int.

getQueryStrand

public StrandedFeature.Strand getQueryStrand()

Return the strand of the sub-hit with respect to the query sequence. This may be null for protein sequences.

Returns:

a Strand.

getSubjectStart

public int getSubjectStart()

Return the start position of the sub-hit in the subject sequence.

Returns:

an int.

getSubjectEnd

public int getSubjectEnd()

Return the start position of the sub-hit in the subject sequence.

Returns:

an int.

getSubjectStrand

public StrandedFeature.Strand getSubjectStrand()

Return the strand of the sub-hit with respect to the subject sequence. This may be null for protein sequences.

Returns:

a Strand.

getAlignment

public Alignment 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.