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 */
021package org.biojava.nbio.core.alignment.matrices;
022
023import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
024import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
025
026
027public interface AAIndexProvider {
028
029         /**
030          * Gets a substitution matrix by its name. The matrices are defined in
031            {@code}src/main/resources/matrices/AAINDEX.txt{@code}
032          * @param matrixName
033          * @return The @{code}SubstitutionMatrix{@code} or null if not exists
034          */
035         SubstitutionMatrix<AminoAcidCompound> getMatrix(String matrixName);
036}