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 * Created on 01-21-2010
021 */
022
023package org.biojava.nbio.core.sequence.features;
024
025import org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader;
026
027import java.util.LinkedHashMap;
028
029/**
030 * If you have a uniprot ID then it is possible to get a collection
031 * of other id(s) that the protein is known by. This is a place holder
032 * for the alternative source database and the id for the same protein.
033 * Currently implement when the {@link UniprotProxySequenceReader} is used
034 * to load a protein sequence
035 *
036 * @author Scooter Willis <willishf at gmail dot com>
037 * @author Paolo Pavan
038 */
039public class DBReferenceInfo extends Qualifier {
040        private LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>();
041        private String database = "";
042        private String id = "";
043
044        /**
045         * The source database and id
046         * @param database
047         * @param id
048         */
049        public DBReferenceInfo(String database, String id){
050                super("db_xref","");
051                this.database = database;
052                this.id = id;
053        }
054
055        /**
056         * Add a property and type to associate with this DBReferenceInfo
057         * @param type
058         * @param value
059         */
060
061        public void addProperty(String type, String value){
062                properties.put(type, value);
063        }
064
065        /**
066         * Get the properties
067         * @return the properties
068         */
069        public LinkedHashMap<String, String> getProperties() {
070                return properties;
071        }
072
073        /**
074         * @param properties the properties to set
075         */
076        public void setProperties(LinkedHashMap<String, String> properties) {
077                this.properties = properties;
078        }
079
080        /**
081         * @return the database
082         */
083        public String getDatabase() {
084                return database;
085        }
086
087        /**
088         * @param database the database to set
089         */
090        public void setDatabase(String database) {
091                this.database = database;
092        }
093
094        /**
095         * @return the id
096         */
097        public String getId() {
098                return id;
099        }
100
101        /**
102         * @param id the id to set
103         */
104        public void setId(String id) {
105                this.id = id;
106        }
107
108        @Override
109        public String toString() {
110                return database + ":" + id + ":" + properties;
111        }
112
113
114
115}