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.genome.homology;
022
023import org.biojava.nbio.genome.query.BlastXMLQuery;
024
025import java.io.File;
026import java.util.ArrayList;
027import java.util.LinkedHashMap;
028
029/**
030 *
031 * @author Scooter Willis <willishf at gmail dot com>
032 */
033public class BlastHomologyHits {
034
035        static public LinkedHashMap<String, ArrayList<String>> getMatches(File xmlBlastHits, double ecutoff) throws Exception {
036                LinkedHashMap<String, ArrayList<String>> homologyHits = new LinkedHashMap<String, ArrayList<String>>();
037                BlastXMLQuery blastXMLQuery = new BlastXMLQuery(xmlBlastHits.getAbsolutePath());
038                LinkedHashMap<String, ArrayList<String>> hits = blastXMLQuery.getHitsQueryDef(ecutoff);
039                for (String accessionid : hits.keySet()) {
040                        String[] data = accessionid.split(" "); // deal with notes/comments in blast results
041                        String id = data[0];
042                        ArrayList<String> uniprotProteinHits = hits.get(accessionid);
043                        homologyHits.put(id, uniprotProteinHits);
044
045                }
046                return homologyHits;
047        }
048}