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.alignment.Alignments.PairInProfileScorerType; 027import org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType; 028import org.biojava.nbio.core.sequence.template.Compound; 029import org.biojava.nbio.core.sequence.template.Sequence; 030 031/** 032 * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and 033 * realigning. 034 * 035 * @author Mark Chapman 036 * @param <S> each element of the alignment {@link Profile} is of type S 037 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C 038 */ 039public interface RescoreRefiner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C> { 040 041 /** 042 * Returns class type of pairwise scoring subroutine. 043 * 044 * @return class type of pairwise scoring subroutine 045 */ 046 PairInProfileScorerType getPairInProfileScorer(); 047 048 /** 049 * Returns class type of profile-profile alignment subroutine. 050 * 051 * @return class type of profile-profile alignment subroutine 052 */ 053 ProfileProfileAlignerType getProfileProfileAligner(); 054 055}