Package org.biojava.bio.search

Interface SeqSimilaritySearchHit

All Superinterfaces:

Annotatable, Changeable

All Known Implementing Classes:

SequenceDBSearchHit, SimpleSeqSimilaritySearchHit

public interface SeqSimilaritySearchHit
extends Annotatable

Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.

Author:

Gerald Loeffler, Keith James

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	SeqSimilaritySearchHit.ByScoreComparator	ByScoreComparator compares SeqSimilaritySearchHits by their score.
static class	SeqSimilaritySearchHit.BySubHitCountComparator	BySubHitCountComparator compares SeqSimilaritySearchHits by their number of sub-hits.

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field	Description
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

Modifier and Type	Method	Description
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.
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.
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

byScore

static final SeqSimilaritySearchHit.ByScoreComparator byScore

byScore contains a SeqSimilaritySearchHit comparator which compares by their score.

bySubHitCount

static final SeqSimilaritySearchHit.BySubHitCountComparator bySubHitCount

bySubHitCount contains a SeqSimilaritySearchHit comparator which compares by their number of sub-hits.

Method Detail

getScore

double getScore()

Return the overall score of this hit in the units defined by the search algorithm.

Returns:

the overall score of this hit. This is a mandatory piece of information and hence may not be NaN.

getPValue

double getPValue()

Return the overall P-value of this hit.

Returns:

the overall P-value of this 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

double getEValue()

Return the overall E-value of this hit.

Returns:

the overall E-value of this 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

int getQueryStart()

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

Returns:

an int.

getQueryEnd

int getQueryEnd()

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

Returns:

an int.

getQueryStrand

StrandedFeature.Strand getQueryStrand()

Return the strand of the hit with respect to the query sequence. If the sub-hits are not all on the same strand this should return the unknown strand. This may be null for protein sequences.

Returns:

a Strand.

getSubjectStart

int getSubjectStart()

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

Returns:

an int.

getSubjectEnd

int getSubjectEnd()

Return the end position of the last sub-hit in the subject sequence.

Returns:

an int.

getSubjectStrand

StrandedFeature.Strand getSubjectStrand()

Return the strand of the sub-hit with respect to the subject sequence. If the sub-hits are not all on the same strand this should return the unknown strand. This may be null for protein sequences.

Returns:

a Strand.

getSubjectID

String getSubjectID()

The sequence identifier of this hit within the sequence database against which the search was performed.

Returns:

the (unique) sequence identifier for this hit, valid within the sequence database against which this search was performed. Never returns null.

getSubHits

List getSubHits()

Return all sub-hits for this sequence similarity search hit. The sub-hits contain concrete alignments (and scores) for sequence stretches from the sequence of this hit. The sub-hits in the list returned by this method are sorted from best to worst.

Returns:

a List of SeqSimilaritySearchSubHit objects containing all sub-hits for this hit. Never returns null and the List is guaranteed to contain at least one entry.