/*
* 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 java.util.List;
import org.biojava.bio.Annotatable;
import org.biojava.bio.seq.StrandedFeature.Strand;
/**
* Objects of this type represent one particular hit (sequence and
* associated information) from a sequence similarity search.
*
* @author Gerald Loeffler
* @author Keith James
*/
public interface SeqSimilaritySearchHit extends Annotatable
{
/**
* Return the overall score of this hit in the units defined by the
* search algorithm.
*
* @return the overall score of this hit. This is a mandatory piece
* of information and hence may not be NaN.
*/
public double getScore();
/**
* Return the overall P-value of this hit.
*
* @return 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.
*/
public double getPValue();
/**
* Return the overall E-value of this hit.
*
* @return 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.
*/
public double getEValue();
/**
* Return the start position of the first sub-hit in the query
* sequence.
*
* @return an int
.
*/
public int getQueryStart();
/**
* Return the end position of the last sub-hit in the query
* sequence.
*
* @return an int
.
*/
public int getQueryEnd();
/**
* 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.
*
* @return a Strand
.
*/
public Strand getQueryStrand();
/**
* Return the start position of the first sub-hit in the subject
* sequence.
*
* @return an int
.
*/
public int getSubjectStart();
/**
* Return the end position of the last 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. If the sub-hits are not all on the same strand this
* should return the unknown strand. This may be null for protein
* sequences.
*
* @return a Strand
.
*/
public Strand getSubjectStrand();
/**
* The sequence identifier of this hit within the sequence
* database against which the search was performed.
*
* @return the (unique) sequence identifier for this hit, valid
* within the sequence database against which this search was
* performed. Never returns null.
*/
public String getSubjectID();
/**
* 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.
* @return 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.
*/
public List getSubHits();
/**
* byScore
contains a
* SeqSimilaritySearchHit
comparator which
* compares by their score.
*/
public static final ByScoreComparator byScore = new ByScoreComparator();
/**
* bySubHitCount
contains a
* SeqSimilaritySearchHit
comparator which
* compares by their number of sub-hits.
*/
public static final BySubHitCountComparator bySubHitCount =
new BySubHitCountComparator();
/**
* ByScoreComparator
compares
* SeqSimilaritySearchHit
s by their score.
*/
public static final class ByScoreComparator implements Comparator
{
public int compare(Object o1, Object o2)
{
SeqSimilaritySearchHit h1 = (SeqSimilaritySearchHit) o1;
SeqSimilaritySearchHit h2 = (SeqSimilaritySearchHit) o2;
if (h1.getScore() > h2.getScore())
return 1;
else if (h1.getScore() < h2.getScore())
return -1;
else
return 0;
}
}
/**
* BySubHitCountComparator
compares
* SeqSimilaritySearchHit
s by their number of
* sub-hits.
*/
public static final class BySubHitCountComparator implements Comparator
{
public int compare(Object o1, Object o2)
{
SeqSimilaritySearchHit h1 = (SeqSimilaritySearchHit) o1;
SeqSimilaritySearchHit h2 = (SeqSimilaritySearchHit) o2;
if (h1.getSubHits().size() > h2.getSubHits().size())
return 1;
else if (h1.getSubHits().size() < h2.getSubHits().size())
return -1;
else
return 0;
}
}
}