/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.search;
import java.util.Comparator;
import org.biojava.bio.Annotatable;
import org.biojava.bio.seq.StrandedFeature.Strand;
import org.biojava.bio.symbol.Alignment;
/**
* 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
* @author Keith James
*/
public interface SeqSimilaritySearchSubHit extends Annotatable
{
/**
* This object is used as the label for the query sequence in the
* alignment of the query sequence with this sub-hit sequence.
*/
public static final String QUERY_LABEL = "Query";
/**
* Return the score of this sub-hit in the units defined by the
* search algorithm.
*
* @return the score of this sub-hit. This is a mandatory piece of
* information and hence may not be NaN.
*/
public double getScore();
/**
* Return the P-value of this sub-hit.
*
* @return 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.
*/
public double getPValue();
/**
* Return the E-value of this sub-hit.
*
* @return 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.
*/
public double getEValue();
/**
* Return the start position of the sub-hit in the query sequence.
*
* @return an int
.
*/
public int getQueryStart();
/**
* Return the end position of the sub-hit in the query sequence.
*
* @return an int
.
*/
public int getQueryEnd();
/**
* Return the strand of the sub-hit with respect to the query
* sequence. This may be null for protein sequences.
*
* @return a Strand
.
*/
public Strand getQueryStrand();
/**
* Return the start position of the sub-hit in the subject
* sequence.
*
* @return an int
.
*/
public int getSubjectStart();
/**
* Return the start position of the sub-hit in the subject
* sequence.
*
* @return an int
.
*/
public int getSubjectEnd();
/**
* Return the strand of the sub-hit with respect to the subject
* sequence. This may be null for protein sequences.
*
* @return a Strand
.
*/
public Strand getSubjectStrand();
/**
* 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.
*
* @return the alignment of the query sequence against this hit
* sequence.
*/
public Alignment getAlignment();
/**
* byScore
contains a
* SeqSimilaritySearchSubHit
comparator which
* compares by the score of the sub-hit.
*/
public static final ByScoreComparator byScore = new ByScoreComparator();
/**
* bySubjectStart
contains a
* SeqSimilaritySearchSubHit
comparator which
* compares by the start position of the sub-hit on the subject
* sequence.
*/
public static final BySubjectStartComparator bySubjectStart
= new BySubjectStartComparator();
/**
* ByScoreComparator
compares
* SeqSimilaritySearchSubHit
s by their score.
*/
public static final class ByScoreComparator implements Comparator
{
public int compare(Object o1, Object o2)
{
SeqSimilaritySearchSubHit h1 = (SeqSimilaritySearchSubHit) o1;
SeqSimilaritySearchSubHit h2 = (SeqSimilaritySearchSubHit) o2;
if (h1.getScore() > h2.getScore())
return 1;
else if (h1.getScore() < h2.getScore())
return -1;
else
return 0;
}
}
/**
* BySubjectStartComparator
compares
* SeqSimilaritySearchSubHit
s by their start position
* on the subject sequence.
*/
public static final class BySubjectStartComparator implements Comparator
{
public int compare(Object o1, Object o2)
{
SeqSimilaritySearchSubHit h1 = (SeqSimilaritySearchSubHit) o1;
SeqSimilaritySearchSubHit h2 = (SeqSimilaritySearchSubHit) o2;
if (h1.getSubjectStart() > h2.getSubjectStart())
return 1;
else if (h1.getSubjectStart() < h2.getSubjectStart())
return -1;
else
return 0;
}
}
}