001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 * Created on June 7, 2010 021 * Author: Mark Chapman 022 */ 023 024package org.biojava.nbio.alignment.template; 025 026import org.biojava.nbio.core.alignment.template.Profile; 027import org.biojava.nbio.core.sequence.template.Compound; 028import org.biojava.nbio.core.sequence.template.Sequence; 029 030/** 031 * Defines an algorithm which computes an alignment {@link Profile} from a list of {@link Sequence}s. 032 * 033 * @author Mark Chapman 034 * @param <S> each element of the alignment {@link Profile} is of type S 035 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C 036 */ 037public interface Aligner<S extends Sequence<C>, C extends Compound> extends Scorer { 038 039 /** 040 * Returns the computation time needed for an alignment computed in nanoseconds. 041 * 042 * @return the computation time in nanoseconds 043 */ 044 long getComputationTime(); 045 046 /** 047 * Returns the alignment {@link Profile} produced by this alignment algorithm. 048 * 049 * @return the alignment profile 050 */ 051 Profile<S, C> getProfile(); 052 053}