org.biojavax.SimpleRichAnnotation 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/
*
*/
/*
* SimpleRichAnnotation.java
*
* Created on July 29, 2005, 10:30 AM
*/
package org.biojavax;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;
import org.biojava.bio.Annotatable;
import org.biojava.ontology.Term;
import org.biojava.utils.AbstractChangeable;
import org.biojava.utils.ChangeEvent;
import org.biojava.utils.ChangeSupport;
import org.biojava.utils.ChangeVetoException;
import org.biojavax.ontology.ComparableTerm;
/**
* Simple annotation wrapper. All non-Note annotations get a rank of zero.
* @author Richard Holland
* @author George Waldon - adapted note change firing
* @since 1.5
*/
public class SimpleRichAnnotation extends AbstractChangeable implements RichAnnotation {
private Set notes = new TreeSet(); // Keeps them ordered by rank then term
/** Creates a new, empty instance of SimpleRichAnnotation */
public SimpleRichAnnotation() {}
/**
* {@inheritDoc}
*/
public void clear() throws ChangeVetoException{
// Use copy of list in order to prevent concurrent modifications.
// Fix for bug #2258.
for(Iterator i = (new ArrayList(this.notes)).iterator(); i.hasNext(); ){
this.removeNote(i.next());
}
}
/**
* {@inheritDoc}
* The map is a copy of the internal structure. It is a map of
* ComparableTerms to Strings corresponding
* to the Term and Value of the Notes in the annotation.
*/
public Map asMap() {
Map m = new TreeMap();
for (Iterator i = this.notes.iterator(); i.hasNext(); ) {
Note n = i.next();
m.put(n.getTerm(), n.getValue());
}
return m;
}
/**
* {@inheritDoc}
* In case the note was already here, a call to ChangeEvent.getPrevious()
* in the firePostChangeEvent method will return a copy of the original note.
*/
public void addNote(Note note) throws ChangeVetoException {
if (note==null) throw new IllegalArgumentException("Note cannot be null");
if(!this.hasListeners(Annotatable.ANNOTATION)) {
this.notes.add(note);
} else {
ChangeEvent ce = new ChangeEvent(
this,
Annotatable.ANNOTATION,
note,
null
);
ChangeSupport cs = this.getChangeSupport(Annotatable.ANNOTATION);
synchronized(cs) {
cs.firePreChangeEvent(ce);
boolean change = this.notes.add(note);
if(!change) {
Note current = null;
Iterator it = notes.iterator();
while(it.hasNext()) {
current = it.next();
if(note.equals(current))
break;
}
Note clone = new SimpleNote(current.getTerm(),current.getValue(),current.getRank());
current.setValue(note.getValue()); //will fire Note.VALUE
ce = new ChangeEvent(
this,
Annotatable.ANNOTATION,
current,
clone
);
}
cs.firePostChangeEvent(ce);
}
}
}
/**
* {@inheritDoc}
*/
public boolean contains(Note note) { return this.notes.contains(note); }
/**
* {@inheritDoc}
* @deprecated
*/
public boolean containsProperty(Object key) {
if (key instanceof Term) key = RichObjectFactory.getDefaultOntology().getOrImportTerm((Term)key);
else key = RichObjectFactory.getDefaultOntology().getOrCreateTerm(key.toString());
for(Iterator i = notes.iterator(); i.hasNext();){
Note n = i.next();
if(n.getTerm().equals(key)) return true;
}
return false;
}
/**
* {@inheritDoc}
*/
public Note getNote(Note note) throws NoSuchElementException {
if (note==null) throw new IllegalArgumentException("Note cannot be null");
for (Iterator i = this.notes.iterator(); i.hasNext(); ) {
Note n = i.next();
if (note.equals(n)) return n;
}
throw new NoSuchElementException("No such property: "+note.getTerm()+", rank "+note.getRank());
}
/**
* {@inheritDoc}
* Strictly it will return the first Note which matches the
* key (or a Term made with a String key)..
* @see #getProperties(Object key)
* @deprecated
*/
public Object getProperty(Object key) throws NoSuchElementException {
if (key instanceof Term) key = RichObjectFactory.getDefaultOntology().getOrImportTerm((Term)key);
else key = RichObjectFactory.getDefaultOntology().getOrCreateTerm(key.toString());
for(Iterator i = notes.iterator(); i.hasNext();){
Note n = i.next();
if (n.getTerm().equals(key)) return n.getValue();
}
throw new NoSuchElementException("No such property: "+key);
}
/**
* {@inheritDoc}
* Strictly it will return all Notes which match the
* key (or a Term made with a String key)..
* @deprecated
*/
public Note[] getProperties(Object key){
if (key instanceof Term) key = RichObjectFactory.getDefaultOntology().getOrImportTerm((Term)key);
else key = RichObjectFactory.getDefaultOntology().getOrCreateTerm(key.toString());
List l = new LinkedList();
for(Iterator i = notes.iterator(); i.hasNext();){
Note n = i.next();
if (n.getTerm().equals(key)) l.add(n);
}
Collections.sort(l);
Note[] na = new Note[l.size()];
l.toArray(na);
return na;
}
/**
* {@inheritDoc}
*/
public Set keys() { return this.asMap().keySet(); }
/**
* {@inheritDoc}
* In case the note is not found, a call to ChangeEvent.getPrevious()
* in the firePostChangeEvent method will return null.
*/
public void removeNote(Note note) throws ChangeVetoException {
if (note==null) throw new IllegalArgumentException("Note cannot be null");
if(!this.hasListeners(Annotatable.ANNOTATION)) {
this.notes.remove(note);
} else {
ChangeEvent ce = new ChangeEvent(
this,
Annotatable.ANNOTATION,
null,
note
);
ChangeSupport cs = this.getChangeSupport(Annotatable.ANNOTATION);
synchronized(cs) {
cs.firePreChangeEvent(ce);
boolean removed = this.notes.remove(note);
if(!removed)
ce = new ChangeEvent(
this,
Annotatable.ANNOTATION,
null,
null
);
cs.firePostChangeEvent(ce);
}
}
}
/**
* {@inheritDoc}
* Strictly it will remove the first Note which matches the
* key (or a Term made with a String key)..
* @deprecated
*/
public void removeProperty(Object key) throws NoSuchElementException, ChangeVetoException {
if (key instanceof Term) key = RichObjectFactory.getDefaultOntology().getOrImportTerm((Term)key);
else key = RichObjectFactory.getDefaultOntology().getOrCreateTerm(key.toString());
for(Iterator i = notes.iterator(); i.hasNext();){
Note n = i.next();
if (n.getTerm().equals(key)) {
this.removeNote(n);
return;
}
}
throw new NoSuchElementException("No such property: "+key);
}
/**
* {@inheritDoc}
* @deprecated
*/
public void setProperty(Object key, Object value) throws IllegalArgumentException, ChangeVetoException {
if(key == null) throw new IllegalArgumentException("Property keys cannot be null");
if (key instanceof Term) key = RichObjectFactory.getDefaultOntology().getOrImportTerm((Term)key);
else key = RichObjectFactory.getDefaultOntology().getOrCreateTerm(key.toString());
this.addNote(new SimpleNote((ComparableTerm)key, (String)(value==null?value:value.toString()), 0));
}
/**
* {@inheritDoc}
* Warning this method gives access to the original
* Collection not a copy. This is required by Hibernate. If you
* modify the object directly the behaviour may be unpredictable.
*/
public Set getNoteSet() { return this.notes; } // original for Hibernate
/**
* {@inheritDoc}
* Warning this method gives access to the original
* Collection not a copy. This is required by Hibernate. If you
* modify the object directly the behaviour may be unpredictable.
*/
public void setNoteSet(Set notes) throws ChangeVetoException { this.notes = notes; } // original for Hibernate
/**
* {@inheritDoc}
* Form: list of "[note]" values separated by commas
*/
public String toString() {
StringBuffer sb = new StringBuffer();
for (Iterator i = this.notes.iterator(); i.hasNext(); ) {
sb.append("[");
sb.append(i.next());
sb.append("]");
if (i.hasNext()) sb.append(",");
}
return sb.toString();
}
}
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