Here is the interface I forgot to send.
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/*
* 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/
*
*/
/*
* Created on 03.08.2005
*
*/
package toolbox.align;
import java.util.LinkedList;
import java.util.List;
import java.util.NoSuchElementException;
import org.biojava.bio.BioException;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.db.SequenceDB;
import org.biojava.bio.symbol.Alignment;
/** This Interface provides methods for the alignment of biosequences.
*
* @author Andreas Dräger
*
*/
public interface SequenceAlignment
{
/**
* @return a string representation of the alignment
* @throws BioException
*/
public String getAlignmentString() throws Exception;
/**
* @param source a SequenceIterator containing a set of sequences to be aligned with
* @param subjectDB the SequenceDB containing another set of sequences.
* @return a list containing the results of all single alignments performed by this
* method.
* @throws NoSuchElementException
* @throws Exception
*/
public List alignAll(SequenceIterator source, SequenceDB subjectDB) throws Exception;
/** Performs a pairwise sequence alignment of the two given sequences.
* @param query
* @param subject
* @return score of the alignment or the distance.
* @throws Exception
*/
public double pairwiseAlignment(Sequence query, Sequence subject) throws Exception;
/** This method also performs a sequence alignment of the two given sequences but it
* returns an Alignment object instead of the score.
* @param query
* @param subject
* @return Alignment
*/
public Alignment getAlignment(Sequence query, Sequence subject) throws Exception;
}
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