/*
* 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.List;
import java.util.Map;
import org.biojava.bio.Annotatable;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.db.SequenceDB;
/**
* Objects of this type represent one particular result of a sequence
* similarity search.
*
* @author Gerald Loeffler
* @author Keith James
*/
public interface SeqSimilaritySearchResult extends Annotatable
{
/**
* Returns the query sequence which was used to perform the search.
*
* @return the Sequence
object used to search the
* SequenceDB
. Never returns null.
*/
public Sequence getQuerySequence();
/**
* Returns the sequence database against which the search was
* performed.
*
* @return the SequenceDB object
against which the
* search was carried out. Never returns null.
*/
public SequenceDB getSequenceDB();
/**
* Returns the search parameters used in the search that produced
* this search result.
*
* @return the (immutable) search parameter Map
* object
. May return null.
*/
public Map getSearchParameters();
/**
* Return all hits in this sequence similarity search result. The
* hits are sorted from best to worst.
*
* @return an (immutable) List
of
* SeqSimilaritySearchHit
objects containing all hits
* in the search result. Never returns null but may return an
* empty list.
*/
public List getHits();
}