private void selectFirstElement() {
// select all if list is not empty
if (root.getChildCount() > 0) {
DefaultMutableTreeNode typeNode = (DefaultMutableTreeNode) root.getFirstChild();
TreePath tp = new TreePath(((DefaultMutableTreeNode) typeNode.getFirstChild()).getPath());
setSelectionPath(tp); // select
}
}
void deleteNodeParent(DefaultMutableTreeNode parent) throws Exception {
while (parent.getChildCount() != 0) {
DefaultMutableTreeNode node = (DefaultMutableTreeNode) parent.getFirstChild();
deleteNodeParent(node);
}
deleteNode(parent);
}
protected void addNewGroup() {
final DefaultMutableTreeNode root =
(DefaultMutableTreeNode)
((DefaultMutableTreeNode) (tree.getModel().getRoot())).getFirstChild();
DefaultMutableTreeNode node = root;
if (node.getChildCount() > 0) {
node = (DefaultMutableTreeNode) node.getFirstChild();
}
if (tree.getSelectionPath() != null) {
node = (DefaultMutableTreeNode) tree.getLastSelectedPathComponent();
}
if (node != root) {
DefaultMutableTreeNode newNode =
new ActivableMutableTreeNode(new Group("group" + node.getParent().getChildCount() + 1));
final DefaultMutableTreeNode parent = (DefaultMutableTreeNode) node.getParent();
parent.insert(newNode, parent.getIndex(node));
newModel.reload();
tree.setSelectionPath(new TreePath(newModel.getPathToRoot(newNode)));
}
}
/**
* Obtiene los nodos seleccionados de un jtree creando una hash de Capas/Atributos
*
* @param jtreeAtributes
* @return
*/
private Map<String, List<String>> getLayersAtributesList(JTree jtreeAtributes) {
Map<String, List<String>> tablaCapasAtributos = new HashMap<String, List<String>>();
List<String> listaAtr = null;
String nombreCapa = null;
String nombreAtributo = null;
DefaultTreeModel model = (DefaultTreeModel) jtreeAtributes.getModel();
DefaultMutableTreeNode root = (DefaultMutableTreeNode) model.getRoot();
DefaultMutableTreeNode chosen = (DefaultMutableTreeNode) root.getFirstChild();
DefaultMutableTreeNode leaf = null;
CheckBoxNode checkNode = null;
for (int i = 0; i < root.getChildCount(); i++) {
nombreCapa = chosen.toString();
leaf = chosen.getFirstLeaf();
for (int j = 0; j < chosen.getLeafCount(); j++) {
checkNode = (CheckBoxNode) leaf.getUserObject();
nombreAtributo = checkNode.getText();
// testeamos si el atributo está seleccionado
if (checkNode.isSelected()) {
if (tablaCapasAtributos.containsKey(nombreCapa)) {
listaAtr = tablaCapasAtributos.get(nombreCapa);
} else {
listaAtr = new ArrayList<String>();
}
listaAtr.add(nombreAtributo);
tablaCapasAtributos.put(nombreCapa, listaAtr);
}
leaf = leaf.getNextLeaf();
}
// si no hay ningun atributo seleccionado guardamos unicamente la capa
if (!tablaCapasAtributos.containsKey(nombreCapa)) {
tablaCapasAtributos.put(nombreCapa, null);
}
chosen = chosen.getNextSibling();
}
return tablaCapasAtributos;
}
/** This will select the intial ligand in the tree and trigger an update */
public void selectInitialLigand() {
String initialLigand = LigandExplorer.sgetModel().getInitialLigand();
DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) ligandJList.getModel().getRoot();
TreePath paths[] = null;
// select initial BIRD molecules
for (int ix = 0; ix < rootNode.getChildCount(); ix++) {
DefaultMutableTreeNode chainNode = (DefaultMutableTreeNode) rootNode.getChildAt(ix);
if (initialLigand != null) {
for (int lx = 0; lx < chainNode.getChildCount(); lx++) {
DefaultMutableTreeNode subNode = (DefaultMutableTreeNode) chainNode.getChildAt(lx);
if (subNode.getUserObject() instanceof Chain) {
Chain chain = (Chain) subNode.getUserObject();
if (isInitialBirdChain(chain, initialLigand)) {
if (paths == null) {
paths = new TreePath[1];
paths[0] = new TreePath(subNode.getPath());
} else {
break;
}
}
}
}
}
}
// select initial chemical components
for (int ix = 0; ix < rootNode.getChildCount(); ix++) {
DefaultMutableTreeNode chainNode = (DefaultMutableTreeNode) rootNode.getChildAt(ix);
if (initialLigand != null) {
for (int lx = 0; lx < chainNode.getChildCount(); lx++) {
DefaultMutableTreeNode residueNode = (DefaultMutableTreeNode) chainNode.getChildAt(lx);
if (residueNode.getUserObject() instanceof Residue) {
Residue residue = (Residue) residueNode.getUserObject();
if (isInitialLigandResidue(residue, initialLigand)) {
Residue[] ligs = new Residue[1];
ligs[0] = residue;
LigandExplorer.sgetSceneController().setLigandResidues(ligs);
// The following code generates an exception in the swing libs
// (see bug PDBWW-1917 PDB ID 1OLN, ligand XBB), most likely because
// the path has null entries, i.e. for the case above.
// if (paths == null) {
// paths = new TreePath[chainNode.getChildCount()];
// }
// paths[lx] = new TreePath(residueNode.getPath());
// Since we are only selecting a single entry, there is no need to pass in an array
// with
// null entries.
if (paths == null) {
paths = new TreePath[1];
paths[0] = new TreePath(residueNode.getPath());
} else {
break;
}
}
}
}
}
}
TreePath rootPath = new TreePath(rootNode);
for (int ix = 0; ix < rootNode.getChildCount(); ix++)
ligandJList.expandPath(rootPath.pathByAddingChild(rootNode.getChildAt(ix)));
if (paths != null) ligandJList.setSelectionPaths(paths);
// set the discovered intial ligand path(s) as selected
else {
DefaultMutableTreeNode firstChainNode = (DefaultMutableTreeNode) rootNode.getFirstChild();
TreePath selectedPath = rootPath.pathByAddingChild(firstChainNode);
selectedPath = selectedPath.pathByAddingChild(firstChainNode.getFirstChild());
ligandJList.setSelectionPath(selectedPath);
// set the first residue in the first chain as selected
// (jeez, this is a lot of work to do something this simple, I might add...)
}
}
