/** {@inheritDoc} */
public void addName(String nameClass, String name)
throws IllegalArgumentException, ChangeVetoException {
if (name == null) throw new IllegalArgumentException("Name cannot be null");
if (nameClass == null) throw new IllegalArgumentException("Name class cannot be null");
SimpleNCBITaxonName n = new SimpleNCBITaxonName(nameClass, name);
if (!this.hasListeners(NCBITaxon.NAMES)) {
if (!this.namesMap.containsKey(nameClass)) this.namesMap.put(nameClass, new TreeSet());
((Set) this.namesMap.get(nameClass)).add(n);
this.names.add(n);
} else {
ChangeEvent ce =
new ChangeEvent(
this,
NCBITaxon.NAMES,
name,
((Set) this.namesMap.get(nameClass)).contains(n) ? name : null);
ChangeSupport cs = this.getChangeSupport(NCBITaxon.NAMES);
synchronized (cs) {
cs.firePreChangeEvent(ce);
if (!this.namesMap.containsKey(nameClass)) this.namesMap.put(nameClass, new TreeSet());
((Set) this.namesMap.get(nameClass)).add(n);
this.names.add(n);
cs.firePostChangeEvent(ce);
}
}
}
public final void setNullModel(Distribution nullModel)
throws IllegalAlphabetException, ChangeVetoException {
if (nullModel.getAlphabet() != getAlphabet()) {
throw new IllegalAlphabetException(
"Could not use distribution "
+ nullModel
+ " as its alphabet is "
+ nullModel.getAlphabet().getName()
+ " and this distribution's alphabet is "
+ getAlphabet().getName());
}
Distribution oldModel = getNullModel();
if (nullModelForwarder != null) {
if (oldModel != null) {
oldModel.removeChangeListener(nullModelForwarder);
}
nullModel.addChangeListener(nullModelForwarder);
}
if (!hasListeners()) {
// if there are no listeners yet, don't go through the overhead of
// synchronized regions or of trying to inform them.
setNullModelImpl(nullModel);
} else {
// OK - so somebody is intereted in me. Do it properly this time.
ChangeEvent ce = new ChangeEvent(this, Distribution.NULL_MODEL, nullModel, oldModel);
ChangeSupport changeSupport = super.getChangeSupport(Distribution.NULL_MODEL);
synchronized (changeSupport) {
changeSupport.firePreChangeEvent(ce);
setNullModelImpl(nullModel);
changeSupport.firePostChangeEvent(ce);
}
}
}
/**
* <code>setRenderer</code> sets the renderer.
*
* @param renderer a <code>PairwiseSequenceRenderer</code>.
* @exception ChangeVetoException if the change is vetoed.
*/
public void setRenderer(PairwiseSequenceRenderer renderer) throws ChangeVetoException {
if (hasListeners()) {
ChangeEvent ce = new ChangeEvent(this, RENDERER, renderer, this.renderer);
ChangeSupport cs = getChangeSupport(RENDERER);
synchronized (cs) {
cs.firePreChangeEvent(ce);
if (this.renderer instanceof Changeable) {
Changeable c = (Changeable) this.renderer;
c.removeChangeListener(rendererForwarder);
}
this.renderer = renderer;
if (renderer instanceof Changeable) {
Changeable c = (Changeable) renderer;
c.addChangeListener(rendererForwarder);
}
cs.firePostChangeEvent(ce);
}
} else {
this.renderer = renderer;
}
}
/** {@inheritDoc} */
public void setRightValue(Integer rightValue) throws ChangeVetoException {
if (!this.hasListeners(NCBITaxon.RIGHTVALUE)) {
this.rightValue = rightValue;
} else {
ChangeEvent ce = new ChangeEvent(this, NCBITaxon.RIGHTVALUE, rightValue, this.rightValue);
ChangeSupport cs = this.getChangeSupport(NCBITaxon.RIGHTVALUE);
synchronized (cs) {
cs.firePreChangeEvent(ce);
this.rightValue = rightValue;
cs.firePostChangeEvent(ce);
}
}
}
/** {@inheritDoc} */
public void setGeneticCode(Integer geneticCode) throws ChangeVetoException {
if (!this.hasListeners(NCBITaxon.GENETICCODE)) {
this.geneticCode = geneticCode;
} else {
ChangeEvent ce = new ChangeEvent(this, NCBITaxon.GENETICCODE, nodeRank, this.nodeRank);
ChangeSupport cs = this.getChangeSupport(NCBITaxon.GENETICCODE);
synchronized (cs) {
cs.firePreChangeEvent(ce);
this.geneticCode = geneticCode;
cs.firePostChangeEvent(ce);
}
}
}
/**
* Setter for property nodeRank.
*
* @param nodeRank New value of property nodeRank.
* @throws org.biojava.utils.ChangeVetoException in case of objections.
*/
public void setNodeRank(String nodeRank) throws ChangeVetoException {
if (!this.hasListeners(NCBITaxon.NODERANK)) {
this.nodeRank = nodeRank;
} else {
ChangeEvent ce = new ChangeEvent(this, NCBITaxon.NODERANK, nodeRank, this.nodeRank);
ChangeSupport cs = this.getChangeSupport(NCBITaxon.NODERANK);
synchronized (cs) {
cs.firePreChangeEvent(ce);
this.nodeRank = nodeRank;
cs.firePostChangeEvent(ce);
}
}
}
/** {@inheritDoc} */
public void setParentNCBITaxID(Integer parent) throws ChangeVetoException {
if (!this.hasListeners(NCBITaxon.PARENT)) {
this.parent = parent;
} else {
ChangeEvent ce = new ChangeEvent(this, NCBITaxon.PARENT, parent, this.parent);
ChangeSupport cs = this.getChangeSupport(NCBITaxon.PARENT);
synchronized (cs) {
cs.firePreChangeEvent(ce);
this.parent = parent;
cs.firePostChangeEvent(ce);
}
}
}
/**
* <code>setFilter</code> sets the filter.
*
* @param filter a <code>FeatureFilter</code>.
* @exception ChangeVetoException if the change is vetoed.
*/
public void setFilter(FeatureFilter filter) throws ChangeVetoException {
if (hasListeners()) {
ChangeSupport cs = getChangeSupport(FILTER);
synchronized (cs) {
ChangeEvent ce = new ChangeEvent(this, FILTER, this.filter, filter);
cs.firePreChangeEvent(ce);
this.filter = filter;
cs.firePostChangeEvent(ce);
}
} else {
this.filter = filter;
}
}
/**
* <code>setRecurse</code> sets the recursion flag on the filter.
*
* @param recurse a <code>boolean</code>.
* @exception ChangeVetoException if the change is vetoed.
*/
public void setRecurse(boolean recurse) throws ChangeVetoException {
if (hasListeners()) {
ChangeSupport cs = getChangeSupport(RECURSE);
synchronized (cs) {
ChangeEvent ce =
new ChangeEvent(this, RECURSE, new Boolean(recurse), new Boolean(this.recurse));
cs.firePreChangeEvent(ce);
this.recurse = recurse;
cs.firePostChangeEvent(ce);
}
} else {
this.recurse = recurse;
}
}
/*
* (non-Javadoc)
* @see com.bioperception.bio.taxa.NCBITaxon2#setTaxonHidden(boolean)
*/
public final void setTaxonHidden(final boolean isTaxonHidden) throws ChangeVetoException {
if (!this.hasListeners(HIDDEN)) {
this.isTaxonHidden = isTaxonHidden;
} else {
final ChangeEvent ce =
new ChangeEvent(
this, HIDDEN, new Boolean(isTaxonHidden), new Boolean(this.isTaxonHidden));
final ChangeSupport cs = this.getChangeSupport(HIDDEN);
synchronized (cs) {
cs.firePreChangeEvent(ce);
this.isTaxonHidden = isTaxonHidden;
cs.firePostChangeEvent(ce);
}
}
}
/**
* Set the weight of a given symbol in this distribution.
*
* <p>This implementation informs all listeners of the change, and then calls setWeightImpl to
* make the actual change. Sub-classes should over-ride setWeightImpl to implement the actual
* storage of the weights.
*
* @param sym the Symbol to set the weight for
* @param weight it's new weight
* @throws IllegalSymbolException if sym is not known
* @throws ChangeVetoException if the update was prevented
*/
public final void setWeight(Symbol sym, double weight)
throws IllegalSymbolException, ChangeVetoException {
if (!hasListeners()) {
doSetWeight(sym, weight);
} else {
ChangeEvent ce =
new ChangeEvent(
this,
Distribution.WEIGHTS,
new Object[] {sym, new Double(weight)},
new Object[] {sym, new Double(getWeight(sym))});
ChangeSupport changeSupport = super.getChangeSupport(Distribution.WEIGHTS);
synchronized (changeSupport) {
changeSupport.firePreChangeEvent(ce);
doSetWeight(sym, weight);
changeSupport.firePostChangeEvent(ce);
}
}
}
public void setProperty(Object key, Object value) throws ChangeVetoException {
if (!hasListeners()) {
getProperties().put(key, value);
} else {
Map properties = getProperties();
ChangeEvent ce =
new ChangeEvent(
this,
Annotation.PROPERTY,
new Object[] {key, value},
new Object[] {key, properties.get(key)});
ChangeSupport cs = getChangeSupport(Annotation.PROPERTY);
synchronized (cs) {
cs.firePreChangeEvent(ce);
properties.put(key, value);
cs.firePostChangeEvent(ce);
}
}
}
/** {@inheritDoc} */
public boolean removeName(String nameClass, String name)
throws IllegalArgumentException, ChangeVetoException {
if (name == null) throw new IllegalArgumentException("Name cannot be null");
if (nameClass == null) throw new IllegalArgumentException("Name class cannot be null");
SimpleNCBITaxonName n = new SimpleNCBITaxonName(nameClass, name);
if (!this.namesMap.containsKey(nameClass)) return false;
boolean results;
if (!this.hasListeners(NCBITaxon.NAMES)) {
results = ((Set) this.namesMap.get(nameClass)).remove(n);
this.names.remove(n);
} else {
ChangeEvent ce = new ChangeEvent(this, NCBITaxon.NAMES, null, name);
ChangeSupport cs = this.getChangeSupport(NCBITaxon.NAMES);
synchronized (cs) {
cs.firePreChangeEvent(ce);
results = ((Set) this.namesMap.get(nameClass)).remove(n);
this.names.remove(n);
cs.firePostChangeEvent(ce);
}
}
return results;
}
public void removeProperty(Object key) throws ChangeVetoException, NoSuchElementException {
if (!getProperties().containsKey(key)) {
throw new NoSuchElementException("Can't remove key " + key.toString());
}
if (!hasListeners()) {
getProperties().remove(key);
} else {
Map properties = getProperties();
ChangeEvent ce =
new ChangeEvent(
this,
Annotation.PROPERTY,
new Object[] {key, null},
new Object[] {key, properties.get(key)});
ChangeSupport cs = getChangeSupport(Annotation.PROPERTY);
synchronized (cs) {
cs.firePreChangeEvent(ce);
properties.remove(key);
cs.firePostChangeEvent(ce);
}
}
}