org.biojavax.SimpleRankedDocRef Maven / Gradle / Ivy
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojavax;
import org.biojava.bio.seq.io.ParseException;
import org.biojava.utils.AbstractChangeable;
import org.biojava.utils.ChangeEvent;
import org.biojava.utils.ChangeSupport;
import org.biojava.utils.ChangeVetoException;
import org.biojavax.bio.seq.RichLocation;
import org.biojavax.bio.seq.SimplePosition;
import org.biojavax.bio.seq.SimpleRichLocation;
import org.biojavax.bio.seq.io.GenbankLocationParser;
/**
* Represents a documentary reference.
* @author Richard Holland
* @author gwaldon
* @since 1.5
*/
public class SimpleRankedDocRef extends AbstractChangeable implements RankedDocRef {
private DocRef docref;
private Integer start;
private Integer end;
private RichLocation location;
private int rank;
/**
* Constructs a new docref for a given location. If one or the other
* of start and end are null, only the non-null value is used. If both
* are null, no value is used for the location.
* @param docref the document reference. Must not be null.
* @param start the start position of the location.
* @param end the end position of the location.
*/
public SimpleRankedDocRef(DocRef docref, Integer start, Integer end, int rank) {
if (docref==null) throw new IllegalArgumentException("Document reference cannot be null");
this.docref = docref;
this.setStart(start);
this.setEnd(end);
this.rank = rank;
}
/**
* Constructs a new docref for a given location.
* @param docref the document reference. Must not be null.
* @param location the position of the document reference. Must not be null.
*/
public SimpleRankedDocRef(DocRef docref, RichLocation location, int rank) {
if (docref==null) throw new IllegalArgumentException("Document reference cannot be null");
this.docref = docref;
this.makeLocation(location);
this.rank = rank;
}
// Hibernate requirement - not for public use.
protected SimpleRankedDocRef() {}
/**
* {@inheritDoc}
*/
public void setRank(int rank) throws ChangeVetoException {
if(rank==this.rank)
return;
if(!this.hasListeners(RankedDocRef.RANK)) {
this.rank = rank;
} else {
ChangeEvent ce = new ChangeEvent(
this,
RankedDocRef.RANK,
new Integer(rank),
new Integer(this.rank)
);
ChangeSupport cs = this.getChangeSupport(RankedDocRef.RANK);
synchronized(cs) {
cs.firePreChangeEvent(ce);
this.rank = rank;
cs.firePostChangeEvent(ce);
}
}
}
/**
* {@inheritDoc}
*/
public int getRank() { return this.rank; }
/**
* {@inheritDoc}
*/
public DocRef getDocumentReference() { return this.docref; }
/**
* {@inheritDoc}
*/
public Integer getStart() { return this.start; }
/**
* {@inheritDoc}
*/
public Integer getEnd() { return this.end; }
// Hibernate requirement - not for public use.
void setDocumentReference(DocRef docref) { this.docref = docref; }
// Hibernate requirement - not for public use.
private void setStart(Integer start) {
this.start = start;
this.createLocation();
}
// Hibernate requirement - not for public use.
private void setEnd(Integer end) {
this.end = end;
this.createLocation();
}
// Internal use only.
private void createLocation() {
if (this.start==null && this.end==null) location = RichLocation.EMPTY_LOCATION;
else if (this.start==null) location = new SimpleRichLocation(null, new SimplePosition(this.end.intValue()), 0);
else if (this.end==null) location = new SimpleRichLocation(new SimplePosition(this.start.intValue()), null, 0);
else location = new SimpleRichLocation(new SimplePosition(this.start.intValue()), new SimplePosition(this.end.intValue()), 0);
}
// Internal use only.
private void makeLocation(RichLocation location) {
if (location==null)
throw new IllegalArgumentException("Document location cannot be null");
this.location = location;
this.start = new Integer(location.getMin());
this.end = new Integer(location.getMax());
}
/**
* {@inheritDoc}
*/
public void setLocation(RichLocation location) throws ChangeVetoException {
if(!this.hasListeners(RankedDocRef.LOCATION)) {
makeLocation(location);
} else {
ChangeEvent ce = new ChangeEvent(
this,
RankedDocRef.LOCATION,
location,
this.location
);
ChangeSupport cs = this.getChangeSupport(RankedDocRef.LOCATION);
synchronized(cs) {
cs.firePreChangeEvent(ce);
makeLocation(location);
cs.firePostChangeEvent(ce);
}
}
}
public RichLocation getLocation() {
return this.location;
}
// Internal use only.
final void setLocationText(final String theLocation) throws ParseException {
if (theLocation == null) {
makeLocation(RichLocation.EMPTY_LOCATION);
} else {
final RichLocation location = GenbankLocationParser.parseLocation(RichObjectFactory.getDefaultNamespace(), null, theLocation);
makeLocation(location);
}
}
// Internal use only.
final String getLocationText() {
return getLocation() == RichLocation.EMPTY_LOCATION?null:GenbankLocationParser.writeLocation(getLocation());
}
/**
* {@inheritDoc}
* Two ranked document references are equal if they have the same rank
* and refer to the same location and same document reference.
*/
public boolean equals(Object obj) {
if (this == obj) return true;
if (obj==null || !(obj instanceof RankedDocRef)) return false;
// Hibernate comparison - we haven't been populated yet
if (this.docref==null) return false;
// Normal comparison
RankedDocRef them = (RankedDocRef)obj;
return (this.rank==them.getRank() &&
this.location.equals(them.getLocation()) &&
this.docref.equals(them.getDocumentReference()));
}
/**
* {@inheritDoc}
* Ranked document references are sorted first by rank then location
* then by actual document reference.
*/
public int compareTo(Object o) {
if (o==this) return 0;
// Hibernate comparison - we haven't been populated yet
if (this.docref==null) return -1;
// Normal comparison
RankedDocRef them = (RankedDocRef)o;
if (this.rank!=them.getRank()) return this.rank - them.getRank();
if (!this.location.equals(them.getLocation())) return this.location.compareTo(them.getLocation());
return this.docref.compareTo(them.getDocumentReference());
}
/**
* {@inheritDoc}
*/
public int hashCode() {
int code = 17;
// Hibernate comparison - we haven't been populated yet
if (this.docref==null) return code;
// Normal comparison
code = 37*code + this.docref.hashCode();
code = 37*code + this.location.hashCode();
code = 37*code + this.rank;
return code;
}
/**
* {@inheritDoc}
* Form: "(#rank) docref"
*/
public String toString() {
return "(#"+this.rank+") "+this.docref;
}
}
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