void delete(AnnotationSet annotationSet) {
if (annotationSets.remove(annotationSet)) {
// if the active set was deleted then we need to unselect it
if (activeSet.isPresent() && activeSet.get().equals(annotationSet)) {
activeSet = Optional.empty();
parent.postEvent(new ModelEvents.AnnotationSetSelected(this, Optional.empty()));
}
parent.postEvent(new ModelEvents.AnnotationSetDeleted(annotationSet));
}
}
/**
* Swaps the order of the two annotation sets. The two annotation sets must be distinct and must
* be contained in this network view set, otherwise this method does nothing.
*/
public void swap(AnnotationSet first, AnnotationSet second) {
int i1 = annotationSets.indexOf(first);
int i2 = annotationSets.indexOf(second);
if (i1 < 0 || i2 < 0 || i1 == i2) return;
Collections.swap(annotationSets, i1, i2);
parent.postEvent(new ModelEvents.NetworkViewSetChanged(this, Type.ANNOTATION_SET_ORDER));
}
AnnotationSet build(AnnotationSetBuilder builder) {
AnnotationSet as = new AnnotationSet(this, builder);
annotationSets.add(as);
try {
builder.getCallback().ifPresent(callback -> callback.accept(as));
} catch (Exception e) {
e.printStackTrace();
}
parent.postEvent(new ModelEvents.AnnotationSetAdded(as));
return as;
}
/**
* Sets the given AnnotationSet as the "selected" one. If null is passed then all AnnotationSets
* will be unselected.
*
* <p>Note: Currently switching selection is not supported when the currently selected
* AnnotationSet has collapsed clusters. It is the responsibility of the UI to expand all the
* clusters before switching the AnnotationSet.
*
* <p>MKTODO: It would be better for the model to handle expanding the clusters, but for now we
* will force the UI to do it.
*
* @throws IllegalStateException If the currently active AnnotationSet has collapsed clusters.
*/
public void select(AnnotationSet annotationSet) {
if (annotationSet == null || annotationSets.contains(annotationSet)) {
if (Optional.ofNullable(annotationSet).equals(activeSet)) {
return;
}
if (activeSet.map(AnnotationSet::hasCollapsedCluster).orElse(false)) {
throw new IllegalStateException("Current AnnotationSet has collapsed clusters");
}
CyNetwork network = networkView.getModel();
activeSet = Optional.ofNullable(annotationSet);
// ModelManager.handle(AboutToRemoveNodesEvent) only removes nodes from the active annotation
// set.
// When switching to a new annotation set we need to "fix" the clusters to remove any nodes
// that
// were deleted previously.
// MKTODO: probably need to test for deleted nodes when serializing the model
if (annotationSet != null) {
Set<Cluster> clusters = annotationSet.getClusters();
for (Cluster cluster :
new HashSet<>(
clusters)) { // avoid ConcurrentModificationException because removeNodes() can call
// delete()
Set<CyNode> nodesToRemove =
cluster
.getNodes()
.stream()
.filter(node -> !network.containsNode(node))
.collect(Collectors.toSet());
// Fires ClusterChangedEvent, UI listeners should test if the cluster is part of the
// active annotation set.
if (!nodesToRemove.isEmpty()) {
cluster.removeNodes(nodesToRemove);
}
}
}
parent.postEvent(new ModelEvents.AnnotationSetSelected(this, activeSet));
}
}
public AnnotationSet createAnnotationSet(String name, String labelColumn) {
AnnotationSet as = new AnnotationSet(this, name, labelColumn);
annotationSets.add(as);
parent.postEvent(new ModelEvents.AnnotationSetAdded(as));
return as;
}
