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}