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Noor Almbaidin
committed
add classes of new feature parser for embl file
1 parent a7216ef commit 68dffbb

4 files changed

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

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package org.biojava.nbio.core.sequence.io.embl;
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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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public EmblId() {
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}
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public String getPrimaryAccession() {
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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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}
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public String getSequenceVersion() {
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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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}
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public String getTopology() {
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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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}
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public String getMoleculeType() {
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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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}
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public String getDataClass() {
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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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}
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public String getTaxonomicDivision() {
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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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}
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public String getSequenceLength() {
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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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}
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}

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

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package org.biojava.nbio.core.sequence.io.embl;
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import java.io.*;
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public class EmblParser {
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private File file;
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private EmblId id;
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private EmblReference emblReference;
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private String accessionNumber;
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private String ProjectIdentifier;
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private String createdDate;
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private String lastUpdatedDate;
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private String sequenceDescription;
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private String keyword;
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private String organismSpecies;
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private String organismClassification;
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private String databaseCrossReference;
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private String assemblyHeader;
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private String assemblyInformation;
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private String CON;
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private String sequenceHeader;
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private StringBuilder sequence;
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public EmblId getEmblId() {
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return id;
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}
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public EmblReference getEmblReference() {
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return emblReference;
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}
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public String getAccessionNumber() {
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return accessionNumber;
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}
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public void setAccessionNumber(String accessionNumber) {
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this.accessionNumber = accessionNumber;
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}
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public String getProjectIdentifier() {
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return ProjectIdentifier;
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}
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public void setProjectIdentifier(String projectIdentifier) {
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ProjectIdentifier = projectIdentifier;
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}
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public String getCreatedDate() {
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return createdDate;
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}
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public void setCreatedDate(String createdDate) {
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this.createdDate = createdDate;
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}
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public String getLastUpdatedDate() {
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return lastUpdatedDate;
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}
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public void setLastUpdatedDate(String lastUpdatedDate) {
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this.lastUpdatedDate = lastUpdatedDate;
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}
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public String getSequenceDescription() {
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return sequenceDescription;
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}
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public void setSequenceDescription(String sequenceDescription) {
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this.sequenceDescription = sequenceDescription;
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}
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public String getKeyword() {
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return keyword;
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}
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public void setKeyword(String keyword) {
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this.keyword = keyword;
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}
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public String getOrganismSpecies() {
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return organismSpecies;
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}
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public void setOrganismSpecies(String organismSpecies) {
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this.organismSpecies = organismSpecies;
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}
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public String getOrganismClassification() {
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return organismClassification;
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}
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public void setOrganismClassification(String organismClassification) {
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this.organismClassification = organismClassification;
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}
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public String getDatabaseCrossReference() {
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return databaseCrossReference;
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}
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public void setDatabaseCrossReference(String databaseCrossReference) {
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this.databaseCrossReference = databaseCrossReference;
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}
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public String getAssemblyHeader() {
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return assemblyHeader;
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}
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public void setAssemblyHeader(String assemblyHeader) {
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this.assemblyHeader = assemblyHeader;
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}
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public String getAssemblyInformation() {
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return assemblyInformation;
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}
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public void setAssemblyInformation(String assemblyInformation) {
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this.assemblyInformation = assemblyInformation;
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}
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public String getCON() {
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return CON;
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}
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public void setCON(String CON) {
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this.CON = CON;
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}
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public String getSequenceHeader() {
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return sequenceHeader;
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}
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public void setSequenceHeader(String sequenceHeader) {
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this.sequenceHeader = sequenceHeader;
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}
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public StringBuilder getSequence() {
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return sequence;
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}
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public void setSequence(StringBuilder sequence) {
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this.sequence = sequence;
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}
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public EmblParser(File file) {
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setFile(file);
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}
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public void setFile(File file) {
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if (file == null)
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throw new NullPointerException("file can't be null");
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this.file = file;
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}
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public void parse() {
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try (FileReader fileReader = new FileReader(file)) {
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String line = "";
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try (BufferedReader bufferedReader = new BufferedReader(fileReader)) {
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while (bufferedReader.readLine() != null)
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line = bufferedReader.readLine();
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if (line.substring(0, 2).equals("ID"))
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populateID(line);
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}
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} catch (FileNotFoundException e) {
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e.printStackTrace();
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} catch (IOException e) {
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e.printStackTrace();
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}
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}
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private void populateID(String line) {
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}
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}

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

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package org.biojava.nbio.core.sequence.io.embl;
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public class EmblReference {
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private String referenceNumber;
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private String referenceComment;
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private String referencePosition;
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private String referenceCrossReference;
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private String referenceGroup;
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private String referenceAuthor;
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private String referenceTitle;
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private String referenceLocation;
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public String getReferenceNumber() {
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return referenceNumber;
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}
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public void setReferenceNumber(String referenceNumber) {
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this.referenceNumber = referenceNumber;
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}
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public String getReferenceComment() {
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return referenceComment;
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}
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public void setReferenceComment(String referenceComment) {
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this.referenceComment = referenceComment;
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}
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public String getReferencePosition() {
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return referencePosition;
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}
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public void setReferencePosition(String referencePosition) {
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this.referencePosition = referencePosition;
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}
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public String getReferenceCrossReference() {
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return referenceCrossReference;
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}
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public void setReferenceCrossReference(String referenceCrossReference) {
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this.referenceCrossReference = referenceCrossReference;
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}
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public String getReferenceGroup() {
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return referenceGroup;
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}
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public void setReferenceGroup(String referenceGroup) {
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this.referenceGroup = referenceGroup;
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}
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public String getReferenceAuthor() {
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return referenceAuthor;
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}
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public void setReferenceAuthor(String referenceAuthor) {
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this.referenceAuthor = referenceAuthor;
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}
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public String getReferenceTitle() {
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return referenceTitle;
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}
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public void setReferenceTitle(String referenceTitle) {
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this.referenceTitle = referenceTitle;
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}
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public String getReferenceLocation() {
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return referenceLocation;
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}
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public void setReferenceLocation(String referenceLocation) {
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this.referenceLocation = referenceLocation;
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}
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}

‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/embl/EmblParserTest.java‎

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package org.biojava.nbio.core.sequence.io.embl;
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import org.junit.Test;
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import java.io.File;
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public class EmblParserTest {
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@Test(expected = NullPointerException.class)
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public void givenNullFileParameterWhenCreateEmblParserThenthrowException(){
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File file = null;
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EmblParser emblParser = new EmblParser(file);
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}
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@Test
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public void test(){
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File file = new File("/home/pslpt219/Desktop/Homo.dat");
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EmblParser emblParser = new EmblParser(file);
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emblParser.parse();
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}
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}

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