public synchronized void swap(RootedTree destTree, PhyloNode destNode) {
synchronized (destTree) {
/*
* If we're swapping within the same tree, then it's easy:
*/
if (origTree == destTree && origVertex != null) {
Object p1 = origTree.getParentOf(origVertex);
Object p2 = origTree.getParentOf(destNode);
if (p1 != null && p2 != null) {
origTree.removeEdge(p1, origVertex);
origTree.removeEdge(p2, destNode);
origTree.addEdge(p1, destNode);
origTree.addEdge(p2, origVertex);
}
} else {
/*
* If we're swapping with an "external" clipboard, then it's also easy.
*/
PhyloTree clipTree = loadClip();
setClip(destTree, destNode);
setClipFromJS(newickString);
Object p1 = destTree.getParentOf(destNode);
destTree.deleteSubtree(destNode);
Graphs.addGraph(destTree, clipTree);
if (p1 == null) {
destTree.setRoot(clipTree.getRoot());
} else {
destTree.addEdge(p1, clipTree.getRoot());
}
}
}
}
public void setClip(RootedTree tree, PhyloNode node) {
setStateRecursive(tree, (PhyloNode) tree.getRoot(), PhyloNode.NONE);
RootedTree clone = tree.cloneSubtree(node);
newickString = TreeIO.createNHXString(clone);
origTree = tree;
origVertex = node;
fireEvent(CLIPBOARD_UPDATED);
}
void clearCutNodes() {
if (origTree != null) {
if (origVertex != null && origVertex.getState() == PhyloNode.CUT) {
origTree.deleteSubtree(origVertex);
origTree.removeElbowsBelow(origTree.getRoot());
setStateRecursive(origTree, (PhyloNode) origTree.getRoot(), PhyloNode.NONE);
origVertex.found = false;
origVertex = null;
origTree.modPlus();
}
}
}
void clearTree() {
if (origTree != null) {
setStateRecursive(origTree, (PhyloNode) origTree.getRoot(), PhyloNode.NONE);
origTree = null;
}
}