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 023import jdk.nashorn.internal.ir.annotations.Immutable; 024 025/** 026 * This class contains the processed data of embl file 027 * Primary accession number 028 * Sequence version number 029 * Topology: 'circular' or 'linear' 030 * Molecule type 031 * Data class 032 * Taxonomic division 033 * Sequence length 034 * 035 * @author Noor Aldeen Al Mbaidin 036 * @since 5.0.0 037 */ 038@Immutable 039public class EmblId { 040 041 042 private final String primaryAccession; 043 private final String sequenceVersion; 044 private final String topology; 045 private final String moleculeType; 046 private final String dataClass; 047 private final String taxonomicDivision; 048 private final String sequenceLength; 049 050 public EmblId(String primaryAccession, String sequenceVersion, String topology, 051 String moleculeType, String dataClass, String taxonomicDivision, 052 String sequenceLength) { 053 this.primaryAccession = primaryAccession; 054 this.sequenceVersion = sequenceVersion; 055 this.topology = topology; 056 this.moleculeType = moleculeType; 057 this.dataClass = dataClass; 058 this.taxonomicDivision = taxonomicDivision; 059 this.sequenceLength = sequenceLength; 060 } 061 062 /** 063 * @return String 064 */ 065 public String getPrimaryAccession() { 066 return primaryAccession; 067 } 068 069 /** 070 * return the sequence version 071 * 072 * @return String 073 */ 074 public String getSequenceVersion() { 075 return sequenceVersion; 076 } 077 078 public String getTopology() { 079 return topology; 080 } 081 082 /** 083 * Molecule type this represents the type of molecule as stored 084 * 085 * @return String 086 */ 087 public String getMoleculeType() { 088 return moleculeType; 089 } 090 091 public String getDataClass() { 092 return dataClass; 093 } 094 095 /** 096 * @return String 097 */ 098 public String getTaxonomicDivision() { 099 return taxonomicDivision; 100 } 101 102 /** 103 * Sequence length The last item on the ID line is the length of the 104 * sequence (the total number of bases in the sequence). This number includes 105 * base positions reported as present but undetermined (coded as "N"). 106 * 107 * @return String 108 */ 109 public String getSequenceLength() { 110 return sequenceLength; 111 } 112 113}