X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimeraTreeModel.java;fp=src%2Fext%2Fedu%2Fucsf%2Frbvi%2Fstrucviz2%2FChimeraTreeModel.java;h=9ecc6a77845f492fb38f6dc46b3e6ba9b1586e14;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=f3447ce66b171ab740941b0e5e9b0de464c9e824;hpb=619cc880371f3228e6a1fb33c6bfb6e7a7e2622c;p=jalview.git

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java
index f3447ce..9ecc6a7 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraTreeModel.java
@@ -46,149 +46,171 @@ import javax.swing.tree.TreePath;
 // StructureViz imports
 
 /**
- * The ChimeraTreeModel class provides the underlying model
- * for the navigation tree in the ModelNavigatorDialog.
+ * 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);
-		}
-	}	
+ */
+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);
+    }
+  }
 }