/* 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);
    }
  }
}
