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 uiEvent(UIEvent e) { if (e.getID() == UIEvent.TEXT_VALUE) { PhyloWidget.cfg.search = getText(); PhyloTree t = (PhyloTree) PhyloWidget.trees.getTree(); if (t != null) { t.searchAndMarkFound(getText()); } } }
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; }
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(); } }