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 025 * Primary accession number 026 * Sequence version number 027 * Topology: 'circular' or 'linear' 028 * Molecule type 029 * Data class 030 * Taxonomic division 031 * Sequence length 032 * 033 * @author Noor Aldeen Al Mbaidin 034 * @since 5.0.0 035 */ 036public class EmblId { 037 038 039 private final String primaryAccession; 040 private final String sequenceVersion; 041 private final String topology; 042 private final String moleculeType; 043 private final String dataClass; 044 private final String taxonomicDivision; 045 private final String sequenceLength; 046 047 public EmblId(String primaryAccession, String sequenceVersion, String topology, 048 String moleculeType, String dataClass, String taxonomicDivision, 049 String sequenceLength) { 050 this.primaryAccession = primaryAccession; 051 this.sequenceVersion = sequenceVersion; 052 this.topology = topology; 053 this.moleculeType = moleculeType; 054 this.dataClass = dataClass; 055 this.taxonomicDivision = taxonomicDivision; 056 this.sequenceLength = sequenceLength; 057 } 058 059 /** 060 * @return String 061 */ 062 public String getPrimaryAccession() { 063 return primaryAccession; 064 } 065 066 /** 067 * return the sequence version 068 * 069 * @return String 070 */ 071 public String getSequenceVersion() { 072 return sequenceVersion; 073 } 074 075 public String getTopology() { 076 return topology; 077 } 078 079 /** 080 * Molecule type this represents the type of molecule as stored 081 * 082 * @return String 083 */ 084 public String getMoleculeType() { 085 return moleculeType; 086 } 087 088 public String getDataClass() { 089 return dataClass; 090 } 091 092 /** 093 * @return String 094 */ 095 public String getTaxonomicDivision() { 096 return taxonomicDivision; 097 } 098 099 /** 100 * Sequence length The last item on the ID line is the length of the 101 * sequence (the total number of bases in the sequence). This number includes 102 * base positions reported as present but undetermined (coded as "N"). 103 * 104 * @return String 105 */ 106 public String getSequenceLength() { 107 return sequenceLength; 108 } 109 110}