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}