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;
025import org.slf4j.Logger;
026import org.slf4j.LoggerFactory;
027
028import java.io.IOException;
029import java.io.InputStream;
030import java.util.Map;
031
032/** The default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directory
033 *
034 * @author Andreas Prlic
035 *
036 */
037public class DefaultAAIndexProvider implements AAIndexProvider {
038
039        private final static Logger logger = LoggerFactory.getLogger(DefaultAAIndexProvider.class);
040
041        Map<String,SubstitutionMatrix<AminoAcidCompound>> matrices;
042
043        public DefaultAAIndexProvider(){
044
045
046                InputStream inStream = getInputStreamToAAindexFile();
047
048                AAIndexFileParser parser = new AAIndexFileParser();
049
050                try {
051                        parser.parse(inStream);
052                } catch (IOException e){
053                        logger.error("Exception: ", e);
054                }
055
056                matrices = parser.getMatrices();
057
058        }
059
060        @Override
061        public SubstitutionMatrix<AminoAcidCompound> getMatrix(String matrixName) {
062
063                return matrices.get(matrixName);
064
065        }
066
067        public InputStream getInputStreamToAAindexFile(){
068                 return SubstitutionMatrixHelper.class.getResourceAsStream(String.format("/matrices/AAINDEX.txt"));
069        }
070
071}