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Lines changed: 53 additions & 22 deletions
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package org.biojava.nbio.core.sequence.io.embl;
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/**
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* This class should parse the data of embl file identification
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*
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* This class contains the processed data of embl file
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* Primary accession number
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* Sequence version number
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* Topology: 'circular' or 'linear'
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* Molecule type
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* Data class
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* Taxonomic division
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* Sequence length
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* @since 5.0.0
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* @author Noor Aldeen Al Mbaidin
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*/
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public class EmblId {
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private String PrimaryAccession;
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private String SequenceVersion;
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private String Topology;
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private String MoleculeType;
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private String DataClass;
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private String TaxonomicDivision;
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private String SequenceLength;
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private String primaryAccession;
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private String sequenceVersion;
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private String topology;
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private String moleculeType;
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private String dataClass;
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private String taxonomicDivision;
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private String sequenceLength;
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public EmblId() {
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}
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/**
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*
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* @return String
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*/
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public String getPrimaryAccession() {
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return PrimaryAccession;
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return primaryAccession;
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}
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public void setPrimaryAccession(String primaryAccession) {
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PrimaryAccession = primaryAccession;
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this.primaryAccession = primaryAccession;
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}
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/**
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* return the sequence version
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* @return String
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*/
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public String getSequenceVersion() {
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return SequenceVersion;
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return sequenceVersion;
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}
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public void setSequenceVersion(String sequenceVersion) {
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SequenceVersion = sequenceVersion;
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this.sequenceVersion = sequenceVersion;
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}
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public String getTopology() {
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return Topology;
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return topology;
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}
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public void setTopology(String topology) {
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Topology = topology;
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this.topology = topology;
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}
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/**
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* Molecule type this represents the type of molecule as stored
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* @return String
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*/
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public String getMoleculeType() {
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return MoleculeType;
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return moleculeType;
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}
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public void setMoleculeType(String moleculeType) {
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MoleculeType = moleculeType;
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this.moleculeType = moleculeType;
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}
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public String getDataClass() {
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return DataClass;
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return dataClass;
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}
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public void setDataClass(String dataClass) {
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DataClass = dataClass;
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this.dataClass = dataClass;
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}
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/**
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*
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* @return String
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*/
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public String getTaxonomicDivision() {
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return TaxonomicDivision;
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return taxonomicDivision;
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}
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public void setTaxonomicDivision(String taxonomicDivision) {
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TaxonomicDivision = taxonomicDivision;
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this.taxonomicDivision = taxonomicDivision;
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}
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/**
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* Sequence length The last item on the ID line is the length of the
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* sequence (the total number of bases in the sequence). This number includes
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* base positions reported as present but undetermined (coded as "N").
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* @return String
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*/
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public String getSequenceLength() {
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return SequenceLength;
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return sequenceLength;
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}
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public void setSequenceLength(String sequenceLength) {
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SequenceLength = sequenceLength;
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this.sequenceLength = sequenceLength;
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}
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}

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblParser.java‎

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