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.sequence.io.embl; 022 023/** 024 * This class contains the processed data of embl file that 025 * contains the referenceNumber, referenceComment, referencePosition 026 * referenceCrossReference, referenceGroup, referenceAuthor 027 * referenceTitle, referenceLocation 028 * 029 * @author Noor Aldeen Al Mbaidin 030 * @since 5.0.0 031 */ 032public class EmblReference { 033 034 035 private String referenceNumber; 036 private String referenceComment; 037 private String referencePosition; 038 private String referenceCrossReference; 039 private String referenceGroup; 040 private String referenceAuthor; 041 private String referenceTitle; 042 private String referenceLocation; 043 044 /** 045 * The RN (Reference Number) line gives a unique number to each reference 046 * Citation within an entry. This number is used to designate the reference 047 * in comments and in the feature table. 048 * 049 * @return referenceNumber 050 */ 051 public String getReferenceNumber() { 052 return referenceNumber; 053 } 054 055 public void setReferenceNumber(String referenceNumber) { 056 this.referenceNumber = referenceNumber; 057 } 058 059 /** 060 * The RC (Reference Comment) linetype is an optional linetype which appears if 061 * The reference has a comment. 062 * 063 * @return String 064 */ 065 public String getReferenceComment() { 066 return referenceComment; 067 } 068 069 public void setReferenceComment(String referenceComment) { 070 this.referenceComment = referenceComment; 071 } 072 073 /** 074 * The RP (Reference Position) linetype is 075 * an optional linetype which appears if 076 * one or more contiguous base spans of 077 * the presented sequence can be attributed 078 * to the reference in question. 079 * 080 * @return String 081 */ 082 public String getReferencePosition() { 083 return referencePosition; 084 } 085 086 public void setReferencePosition(String referencePosition) { 087 this.referencePosition = referencePosition; 088 } 089 090 /** 091 * The RX (reference cross-reference) linetype is 092 * an optional linetype which appears if 093 * one or more contiguous base spans of the 094 * presented sequence can be attributed 095 * to the reference in question. 096 * 097 * @return String 098 */ 099 public String getReferenceCrossReference() { 100 return referenceCrossReference; 101 } 102 103 public void setReferenceCrossReference(String referenceCrossReference) { 104 this.referenceCrossReference = referenceCrossReference; 105 } 106 107 /** 108 * The RG (Reference Group) lines list the working groups/consortia that 109 * produced the record. 110 * 111 * @return String 112 */ 113 public String getReferenceGroup() { 114 return referenceGroup; 115 } 116 117 public void setReferenceGroup(String referenceGroup) { 118 this.referenceGroup = referenceGroup; 119 } 120 121 /** 122 * The RA (Reference Author) lines list the authors of the paper (or other 123 * work) cited. All of the authors are included, and are listed in the order 124 * given in the paper. 125 * 126 * @return String 127 */ 128 public String getReferenceAuthor() { 129 return referenceAuthor; 130 } 131 132 public void setReferenceAuthor(String referenceAuthor) { 133 this.referenceAuthor = referenceAuthor; 134 } 135 136 /** 137 * The RT (Reference Title) lines give the title of the paper (or other work) as 138 * exactly as is possible given the limitations of computer character sets. 139 * 140 * @return String 141 */ 142 public String getReferenceTitle() { 143 return referenceTitle; 144 } 145 146 public void setReferenceTitle(String referenceTitle) { 147 this.referenceTitle = referenceTitle; 148 } 149 150 /** 151 * The RL (Reference Location) line contains the conventional citation 152 * information for the reference. 153 * 154 * @return String 155 */ 156 public String getReferenceLocation() { 157 return referenceLocation; 158 } 159 160 public void setReferenceLocation(String referenceLocation) { 161 this.referenceLocation = referenceLocation; 162 } 163 164 /** 165 * return copy of EmblReference 166 * 167 * @param emblReference 168 * @return EmblReference 169 */ 170 public EmblReference copyEmblReference(EmblReference emblReference) { 171 EmblReference copy = new EmblReference(); 172 copy.setReferenceAuthor(emblReference.getReferenceAuthor()); 173 copy.setReferenceComment(emblReference.getReferenceComment()); 174 copy.setReferenceCrossReference(emblReference.getReferenceCrossReference()); 175 copy.setReferenceGroup(emblReference.getReferenceGroup()); 176 copy.setReferenceLocation(emblReference.getReferenceLocation()); 177 copy.setReferenceNumber(emblReference.getReferenceNumber()); 178 copy.setReferencePosition(emblReference.getReferencePosition()); 179 copy.setReferenceTitle(emblReference.getReferenceTitle()); 180 return copy; 181 } 182 183}