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 DATE 021 * 022 */ 023package org.biojava.nbio.core.sequence; 024 025import org.biojava.nbio.core.util.Equals; 026import org.biojava.nbio.core.util.Hashcoder; 027 028/** 029 * Used in Sequences as the unique indentifier. If possible, set the {@link DataSource} to know the 030 * source of the id. This allows a SequenceProxy to gather features or related sequences 031 * Protein->Gene as an example. When parsing a Blast file it is also possible 032 * to identify the type of ID 033 * 034 * @author Scooter Willis 035 * @author Jacek Grzebyta 036 */ 037public class AccessionID { 038 039 private String id = null; 040 private DataSource source = DataSource.LOCAL; 041 private Integer version; 042 private String identifier = null; 043 044 /** 045 * 046 */ 047 048 public AccessionID(){ 049 id = ""; 050 051 } 052 053 /** 054 * 055 * @param id 056 */ 057 public AccessionID(String id) { 058 this.id = id.trim(); 059 this.source = DataSource.LOCAL; 060 } 061 062 063 /** 064 * 065 * @param id 066 * @param source 067 */ 068 public AccessionID(String id, DataSource source) { 069 this.id = id.trim(); 070 this.source = source; 071 } 072 073 public AccessionID(String id, DataSource source, Integer version, String identifier) { 074 this.id = id; 075 this.source = source; 076 this.version = version; 077 this.identifier = identifier; 078 } 079 080 /** 081 * @return the id 082 */ 083 public String getID() { 084 return id; 085 } 086 087 /** 088 * @return the source 089 */ 090 public DataSource getDataSource() { 091 return source; 092 } 093 094 @Override 095 public boolean equals(Object o) { 096 boolean equals = false; 097 if (Equals.classEqual(this, o)) { 098 AccessionID l = (AccessionID) o; 099 equals = (Equals.equal(getID(), l.getID()) 100 && Equals.equal(getDataSource(), l.getDataSource()) 101 && Equals.equal(getIdentifier(), l.getIdentifier()) 102 && Equals.equal(getVersion(), l.getVersion())); 103 } 104 return equals; 105 } 106 107 @Override 108 public int hashCode() { 109 int r = Hashcoder.SEED; 110 r = Hashcoder.hash(r, getID()); 111 r = Hashcoder.hash(r, getDataSource()); 112 r = Hashcoder.hash(r, getIdentifier()); 113 r = Hashcoder.hash(r, getVersion()); 114 return r; 115 } 116 117// public void setDataSource(DataSource dataSource){ 118// source = dataSource; 119// } 120 121 122 /** 123 * In case if the {@link #getID() } is not unique keeps the id version. 124 * @return the version 125 */ 126 public Integer getVersion() { 127 return version; 128 } 129 130 public void setVersion(Integer version) { 131 this.version = version; 132 } 133 134 /** 135 * In case if {@link #getID() } in not unique keeps the alternative id, eg. NCBI GI number. 136 * 137 * This may null. 138 * 139 * @return 140 */ 141 public String getIdentifier() { 142 return identifier; 143 } 144 145 public void setIdentifier(String identifier) { 146 this.identifier = identifier; 147 } 148 149 150 @Override 151 public String toString() { 152 return id; 153 } 154}