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 synchronized void paste(CachedRootedTree destTree, PhyloNode destNode) {
// Translate the newick string into a RooteTree.
PhyloTree tree = loadClip();
// Add the clone's vertices and edges to the destination tree.
synchronized (destTree) {
destTree.setHoldCalculations(true);
Graphs.addGraph(destTree, tree);
// Insert the clone's root vertex into the midpoint above destNode.
if (destTree.getParentOf(destNode) == null) {
destTree.addEdge(destNode, tree.getRoot());
} else {
DefaultVertex internalVertex = destTree.createAndAddVertex();
((PhyloNode) internalVertex).setPosition(origVertex);
destTree.insertNodeBetween(destTree.getParentOf(destNode), destNode, internalVertex);
destTree.addEdge(internalVertex, tree.getRoot());
}
destTree.setHoldCalculations(false);
destTree.modPlus();
clearCutNodes();
}
}
PhyloTree loadClip() {
if (newickString == null || newickString.length() == 0) {
/*
* Try loading a tree from the system clipboard.
*/
newickString = StringClipboard.instance.fromClipboard();
}
if (newickString == null || newickString.length() == 0)
throw new Error("Called TreeClipboard.paste() with empty clipboard");
PhyloTree clipTree = new PhyloTree();
TreeIO.parseNewickString(clipTree, newickString);
if (origTree != null && origVertex != null) {
setPositionRecursive(clipTree, (PhyloNode) clipTree.getRoot(), origVertex);
}
return clipTree;
}