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 */
021
022package org.biojava.nbio.genome.parsers.gff;
023
024import java.util.LinkedHashMap;
025
026/**
027 *
028 * @author Scooter Willis <willishf at gmail dot com>
029 */
030public class FeatureHelper {
031
032        /**
033         * Build a list of individual features to allow easy indexing and to avoid iterating through large genome gff3 files
034         * The index for the returned HashMap is the value of the attribute used to build the index
035         * @param attribute
036         * @param list
037         * @return
038         */
039        static public LinkedHashMap<String,FeatureList> buildFeatureAtrributeIndex(String attribute,FeatureList list){
040
041                LinkedHashMap<String,FeatureList> featureHashMap = new LinkedHashMap<String,FeatureList>();
042                FeatureList featureList = list.selectByAttribute(attribute);
043                for(FeatureI feature : featureList){
044                        String value = feature.getAttribute(attribute);
045                        FeatureList features = featureHashMap.get(value);
046                        if(features == null){
047                                features = new FeatureList();
048                                featureHashMap.put(value, features);
049                        }
050                        features.add(feature);
051                }
052
053                return featureHashMap;
054        }
055
056}