org.biojava.nbio.alignment.template.Aligner Maven / Gradle / Ivy
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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 June 7, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment.template;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;
/**
* Defines an algorithm which computes an alignment {@link Profile} from a list of {@link Sequence}s.
*
* @author Mark Chapman
* @param each element of the alignment {@link Profile} is of type S
* @param each element of an {@link AlignedSequence} is a {@link Compound} of type C
*/
public interface Aligner, C extends Compound> extends Scorer {
/**
* Returns the computation time needed for an alignment computed in nanoseconds.
*
* @return the computation time in nanoseconds
*/
long getComputationTime();
/**
* Returns the alignment {@link Profile} produced by this alignment algorithm.
*
* @return the alignment profile
*/
Profile getProfile();
}