--- /dev/null
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package ext.edu.ucsf.rbvi.strucviz2;
+
+// System imports
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.JTree;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.DefaultTreeModel;
+import javax.swing.tree.TreePath;
+// Cytoscape imports
+// StructureViz imports
+
+/**
+ * The ChimeraTreeModel class provides the underlying model
+ * for the navigation tree in the ModelNavigatorDialog.
+ *
+ * @author scooter
+ * @see ModelNavigatorDialog
+ */
+public class ChimeraTreeModel extends DefaultTreeModel {
+ private ChimeraManager chimeraManager;
+ private JTree navigationTree;
+ private int residueDisplay = ChimeraResidue.THREE_LETTER;
+
+ /**
+ * Constructor for the ChimeraTreeModel.
+ *
+ * @param chimeraObject the Chimera object that this tree represents
+ * @param tree the JTree used to display the object
+ * @see Chimera
+ */
+ public ChimeraTreeModel (ChimeraManager chimeraManager, JTree tree) {
+ super(new DefaultMutableTreeNode());
+ this.chimeraManager = chimeraManager;
+ this.navigationTree = tree;
+ DefaultMutableTreeNode rootNode = buildTree();
+ this.setRoot(rootNode);
+ }
+
+ /**
+ * Set the display type for the residues. The display type
+ * must be one of:
+ *
+ * ChimeraResidue.THREE_LETTER
+ * ChimeraResidue.SINGLE_LETTER
+ * ChimeraResidue.FULL_NAME
+ *
+ * @param newDisplay the display type
+ * @see ChimeraResidue
+ */
+ public void setResidueDisplay(int newDisplay) {
+ this.residueDisplay = newDisplay;
+ }
+
+ /**
+ * This method is called to rebuild the tree model "from scratch"
+ */
+ public void reload() {
+ // First, rebuild the tree with the new data
+ DefaultMutableTreeNode rootNode = buildTree();
+ this.setRoot(rootNode);
+
+ // Now let the superclass do all of the work
+ super.reload();
+ }
+
+ /**
+ * Rebuild an existing tree
+ */
+ public void rebuildTree() {
+ DefaultMutableTreeNode rootNode = buildTree();
+ DefaultTreeModel model = (DefaultTreeModel)navigationTree.getModel();
+ model.setRoot(rootNode);
+ model.reload();
+ }
+
+ /**
+ * Build the tree from the current Chimera data
+ *
+ * @return DefaultMutableTreeNode that represents the currently loaded Chimera models
+ */
+ private DefaultMutableTreeNode buildTree() {
+ int modelCount = chimeraManager.getChimeraModelsCount(true);
+ DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(modelCount+" Open Chimera Models");
+ TreePath rootPath = new TreePath(rootNode);
+
+ TreePath path = null;
+ DefaultMutableTreeNode model = null;
+
+ // Add all of the Chimera models
+ for (ChimeraModel chimeraModel: chimeraManager.getChimeraModels()) {
+ model = new DefaultMutableTreeNode(chimeraModel);
+ path = rootPath.pathByAddingChild(model);
+ chimeraModel.setUserData(path);
+ addChainNodes(chimeraModel, model, path);
+ rootNode.add(model);
+ }
+ return rootNode;
+ }
+
+ /**
+ * add chains to a tree model
+ *
+ * @param chimeraModel the ChimeraModel to get the chains from
+ * @param treeModel the tree model to add the chains to
+ * @param treePath the tree path where the chains should be added
+ */
+ private void addChainNodes(ChimeraModel chimeraModel,
+ DefaultMutableTreeNode treeModel,
+ TreePath treePath) {
+ DefaultMutableTreeNode chain = null;
+ TreePath chainPath = null;
+
+ // Get the list of chains
+ Collection<ChimeraChain> chainList = chimeraModel.getChains();
+
+ if (chainList.size() == 0) {
+ // No chains! Just add the residues
+ addResidues(chimeraModel.getResidues(), treeModel, treePath);
+ return;
+ }
+
+ // Iterate over the chains and add the chain and all of
+ // the chain's residues
+ for (ChimeraChain chimeraChain: chainList) {
+ chain = new DefaultMutableTreeNode(chimeraChain);
+ chainPath = treePath.pathByAddingChild(chain);
+ chimeraChain.setUserData(chainPath);
+ addResidues(chimeraChain.getResidues(), chain, chainPath);
+ treeModel.add(chain);
+ }
+ }
+
+ /**
+ * add residues to a tree model
+ *
+ * @param residues the residues to add
+ * @param treeModel the tree model to add the residues to
+ * @param treePath the tree path where the residues should be added
+ */
+ private void addResidues(Collection<ChimeraResidue> residues,
+ DefaultMutableTreeNode treeModel,
+ TreePath treePath) {
+ DefaultMutableTreeNode residue = null;
+ TreePath residuePath = null;
+
+ List<ChimeraResidue> sortedResidues = new ArrayList<ChimeraResidue>(residues);
+ Collections.sort(sortedResidues);
+
+ // Iterate over all residues & add them to the tree
+ for (ChimeraResidue res: sortedResidues) {
+ res.setDisplayType(this.residueDisplay);
+ residue = new DefaultMutableTreeNode(res);
+ residuePath = treePath.pathByAddingChild(residue);
+ res.setUserData(residuePath);
+ treeModel.add(residue);
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff