/*
* 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 June 7, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment.template;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;
/**
* Defines an {@link Aligner} which builds a score matrix during computation.
*
* @author Mark Chapman
* @param <S> each element of the alignment {@link Profile} is of type S
* @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
*/
public interface MatrixAligner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C> {
/**
* Returns the entire score matrix built during alignment. The first dimension has the length of the first (query)
* sequence + 1; the second has the length of the second (target) sequence + 1; the third has length equal to the
* number of scores stored per pairing of an element from each {@link Sequence}.
*
* @return the score matrix
*/
int[][][] getScoreMatrix();
/**
* Returns a depiction of the score matrix as a {@link String}. This may include additional description such as
* labels for each dimension: element from query sequence, element from target sequence, and meaning of each score.
*
* @return the score matrix as a character sequence
*/
String getScoreMatrixAsString();
}