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mkleen wants to merge 4 commits into from
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Add publication references to genbank parser #593

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cf5553a
Add testcases
Oct 14, 2016
897ea0b
Add unknown publication reference type
Oct 18, 2016
3468dce
Add source and organism to sequence
Oct 19, 2016
c61c9d5
Add more fields
Oct 25, 2016
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91 changes: 91 additions & 0 deletions biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/PublicationReference.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,91 @@
package org.biojava.nbio.core.sequence.features;

import java.util.ArrayList;
import java.util.List;

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@lafita lafita Mar 23, 2017

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Could you document this Class with javadoc?

public class PublicationReference {

public enum ReferenceType {
UNKNOWN, PUBMED, PATENT, DIRECT_SUBMISSION;
}

private String id, title, journal;
private ReferenceType referenceType;
private List<PublicationReferenceAuthor> authors = new ArrayList<>();

public String getId() {
return id;
}

public void setId(String id) {
this.id = id;
}

public String getTitle() {
return title;
}

public void setTitle(String title) {
this.title = title;
}

public String getJournal() {
return journal;
}

public void setJournal(String journal) {
this.journal = journal;
}

public ReferenceType getReferenceType() {
return referenceType;
}

public void setReferenceType(ReferenceType referenceType) {
this.referenceType = referenceType;
}

public List<PublicationReferenceAuthor> getAuthors() {
return authors;
}

public void setAuthors(List<PublicationReferenceAuthor> authors) {
this.authors = authors;
}

@Override
public String toString() {
return "PublicationReference{" +
"id='" + id + '\'' +
", title='" + title + '\'' +
", journal='" + journal + '\'' +
", referenceType=" + referenceType +
", authors=" + authors +
'}';
}

@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;

PublicationReference that = (PublicationReference) o;

if (id != null ? !id.equals(that.id) : that.id != null) return false;
if (title != null ? !title.equals(that.title) : that.title != null) return false;
if (journal != null ? !journal.equals(that.journal) : that.journal != null) return false;
if (referenceType != that.referenceType) return false;
return authors != null ? authors.equals(that.authors) : that.authors == null;

}

@Override
public int hashCode() {
int result = id != null ? id.hashCode() : 0;
result = 31 * result + (title != null ? title.hashCode() : 0);
result = 31 * result + (journal != null ? journal.hashCode() : 0);
result = 31 * result + (referenceType != null ? referenceType.hashCode() : 0);
result = 31 * result + (authors != null ? authors.hashCode() : 0);
return result;
}
}
60 changes: 60 additions & 0 deletions ...ore/src/main/java/org/biojava/nbio/core/sequence/features/PublicationReferenceAuthor.java
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@@ -0,0 +1,60 @@
package org.biojava.nbio.core.sequence.features;

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@lafita lafita Mar 23, 2017

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Could you document this Class with javadoc?

public class PublicationReferenceAuthor {

private String firstName, lastName, fullName;

public String getFirstName() {
return firstName;
}

public void setFirstName(String firstName) {
this.firstName = firstName;
}

public String getLastName() {
return lastName;
}

public void setLastName(String lastName) {
this.lastName = lastName;
}

public String getFullName() {
return fullName;
}

public void setFullName(String fullName) {
this.fullName = fullName;
}

@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;

PublicationReferenceAuthor that = (PublicationReferenceAuthor) o;

if (firstName != null ? !firstName.equals(that.firstName) : that.firstName != null) return false;
if (lastName != null ? !lastName.equals(that.lastName) : that.lastName != null) return false;
return fullName != null ? fullName.equals(that.fullName) : that.fullName == null;

}

@Override
public int hashCode() {
int result = firstName != null ? firstName.hashCode() : 0;
result = 31 * result + (lastName != null ? lastName.hashCode() : 0);
result = 31 * result + (fullName != null ? fullName.hashCode() : 0);
return result;
}

@Override
public String toString() {
return "PublicationAuthor{" +
"firstName='" + firstName + '\'' +
", lastName='" + lastName + '\'' +
", fullName='" + fullName + '\'' +
'}';
}
}
10 changes: 10 additions & 0 deletions biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
import org.biojava.nbio.core.sequence.features.AbstractFeature;
import org.biojava.nbio.core.sequence.features.DBReferenceInfo;
import org.biojava.nbio.core.sequence.features.PublicationReference;
import org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface;
import org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface;
import org.biojava.nbio.core.sequence.template.AbstractSequence;
Expand All @@ -45,6 +46,7 @@
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;

/**
* Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the
Expand Down Expand Up @@ -148,6 +150,12 @@ public LinkedHashMap<String,S> process(int max) throws IOException, CompoundNotF
S sequence = (S) sequenceCreator.getSequence(seqString, 0);
genbankParser.getSequenceHeaderParser().parseHeader(genbankParser.getHeader(), sequence);

sequence.setPublicationReference(genbankParser.getPublicationReferences());
sequence.setKeywords(genbankParser.getKeyWords());
sequence.setSource(genbankParser.getSource());
sequence.setOrganism(genbankParser.getOrganism());
sequence.setComment(genbankParser.getComment());

// add features to new sequence
for (String k: genbankParser.getFeatures().keySet()){
for (AbstractFeature f: genbankParser.getFeatures(k)){
Expand All @@ -163,6 +171,8 @@ public LinkedHashMap<String,S> process(int max) throws IOException, CompoundNotF
sequence.setTaxonomy(new TaxonomyID(q.getDatabase()+":"+q.getId(), DataSource.GENBANK));
}



sequences.put(sequence.getAccession().getID(), sequence);
}
br.close();
Expand Down
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