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Coverage Report

  1. Project Clover database Mon Nov 11 2024 15:05:32 GMT
  2. Package ext.edu.ucsf.rbvi.strucviz2

File ChimeraTreeModel.java

 

Coverage histogram

../../../../../img/srcFileCovDistChart0.png
60% of files have more coverage

Code metrics

2
47
7
1
216
95
8
0.17
6.71
7
1.14

Classes

Class Line # Actions
ChimeraTreeModel 55 47 8
0.00%
 

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1    /* vim: set ts=2: */
2    /**
3    * Copyright (c) 2006 The Regents of the University of California.
4    * All rights reserved.
5    *
6    * Redistribution and use in source and binary forms, with or without
7    * modification, are permitted provided that the following conditions
8    * are met:
9    * 1. Redistributions of source code must retain the above copyright
10    * notice, this list of conditions, and the following disclaimer.
11    * 2. Redistributions in binary form must reproduce the above
12    * copyright notice, this list of conditions, and the following
13    * disclaimer in the documentation and/or other materials provided
14    * with the distribution.
15    * 3. Redistributions must acknowledge that this software was
16    * originally developed by the UCSF Computer Graphics Laboratory
17    * under support by the NIH National Center for Research Resources,
18    * grant P41-RR01081.
19    *
20    * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
21    * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
22    * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
23    * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
24    * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
25    * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
26    * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
27    * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
28    * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
29    * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
30    * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
31    *
32    */
33    package ext.edu.ucsf.rbvi.strucviz2;
34   
35    // System imports
36    import java.util.ArrayList;
37    import java.util.Collection;
38    import java.util.Collections;
39    import java.util.List;
40   
41    import javax.swing.JTree;
42    import javax.swing.tree.DefaultMutableTreeNode;
43    import javax.swing.tree.DefaultTreeModel;
44    import javax.swing.tree.TreePath;
45    // Cytoscape imports
46    // StructureViz imports
47   
48    /**
49    * The ChimeraTreeModel class provides the underlying model for the navigation
50    * tree in the ModelNavigatorDialog.
51    *
52    * @author scooter
53    * @see ModelNavigatorDialog
54    */
 
55    public class ChimeraTreeModel extends DefaultTreeModel
56    {
57    private ChimeraManager chimeraManager;
58   
59    private JTree navigationTree;
60   
61    private int residueDisplay = ChimeraResidue.THREE_LETTER;
62   
63    /**
64    * Constructor for the ChimeraTreeModel.
65    *
66    * @param chimeraObject
67    * the Chimera object that this tree represents
68    * @param tree
69    * the JTree used to display the object
70    * @see Chimera
71    */
 
72  0 toggle public ChimeraTreeModel(ChimeraManager chimeraManager, JTree tree)
73    {
74  0 super(new DefaultMutableTreeNode());
75  0 this.chimeraManager = chimeraManager;
76  0 this.navigationTree = tree;
77  0 DefaultMutableTreeNode rootNode = buildTree();
78  0 this.setRoot(rootNode);
79    }
80   
81    /**
82    * Set the display type for the residues. The display type must be one of:
83    *
84    * ChimeraResidue.THREE_LETTER ChimeraResidue.SINGLE_LETTER
85    * ChimeraResidue.FULL_NAME
86    *
87    * @param newDisplay
88    * the display type
89    * @see ChimeraResidue
90    */
 
91  0 toggle public void setResidueDisplay(int newDisplay)
92    {
93  0 this.residueDisplay = newDisplay;
94    }
95   
96    /**
97    * This method is called to rebuild the tree model "from scratch"
98    */
 
99  0 toggle public void reload()
100    {
101    // First, rebuild the tree with the new data
102  0 DefaultMutableTreeNode rootNode = buildTree();
103  0 this.setRoot(rootNode);
104   
105    // Now let the superclass do all of the work
106  0 super.reload();
107    }
108   
109    /**
110    * Rebuild an existing tree
111    */
 
112  0 toggle public void rebuildTree()
113    {
114  0 DefaultMutableTreeNode rootNode = buildTree();
115  0 DefaultTreeModel model = (DefaultTreeModel) navigationTree.getModel();
116  0 model.setRoot(rootNode);
117  0 model.reload();
118    }
119   
120    /**
121    * Build the tree from the current Chimera data
122    *
123    * @return DefaultMutableTreeNode that represents the currently loaded Chimera
124    * models
125    */
 
126  0 toggle private DefaultMutableTreeNode buildTree()
127    {
128  0 int modelCount = chimeraManager.getChimeraModelsCount(true);
129  0 DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(
130    modelCount + " Open Chimera Models");
131  0 TreePath rootPath = new TreePath(rootNode);
132   
133  0 TreePath path = null;
134  0 DefaultMutableTreeNode model = null;
135   
136    // Add all of the Chimera models
137  0 for (ChimeraModel chimeraModel : chimeraManager.getChimeraModels())
138    {
139  0 model = new DefaultMutableTreeNode(chimeraModel);
140  0 path = rootPath.pathByAddingChild(model);
141  0 chimeraModel.setUserData(path);
142  0 addChainNodes(chimeraModel, model, path);
143  0 rootNode.add(model);
144    }
145  0 return rootNode;
146    }
147   
148    /**
149    * add chains to a tree model
150    *
151    * @param chimeraModel
152    * the ChimeraModel to get the chains from
153    * @param treeModel
154    * the tree model to add the chains to
155    * @param treePath
156    * the tree path where the chains should be added
157    */
 
158  0 toggle private void addChainNodes(ChimeraModel chimeraModel,
159    DefaultMutableTreeNode treeModel, TreePath treePath)
160    {
161  0 DefaultMutableTreeNode chain = null;
162  0 TreePath chainPath = null;
163   
164    // Get the list of chains
165  0 Collection<ChimeraChain> chainList = chimeraModel.getChains();
166   
167  0 if (chainList.size() == 0)
168    {
169    // No chains! Just add the residues
170  0 addResidues(chimeraModel.getResidues(), treeModel, treePath);
171  0 return;
172    }
173   
174    // Iterate over the chains and add the chain and all of
175    // the chain's residues
176  0 for (ChimeraChain chimeraChain : chainList)
177    {
178  0 chain = new DefaultMutableTreeNode(chimeraChain);
179  0 chainPath = treePath.pathByAddingChild(chain);
180  0 chimeraChain.setUserData(chainPath);
181  0 addResidues(chimeraChain.getResidues(), chain, chainPath);
182  0 treeModel.add(chain);
183    }
184    }
185   
186    /**
187    * add residues to a tree model
188    *
189    * @param residues
190    * the residues to add
191    * @param treeModel
192    * the tree model to add the residues to
193    * @param treePath
194    * the tree path where the residues should be added
195    */
 
196  0 toggle private void addResidues(Collection<ChimeraResidue> residues,
197    DefaultMutableTreeNode treeModel, TreePath treePath)
198    {
199  0 DefaultMutableTreeNode residue = null;
200  0 TreePath residuePath = null;
201   
202  0 List<ChimeraResidue> sortedResidues = new ArrayList<ChimeraResidue>(
203    residues);
204  0 Collections.sort(sortedResidues);
205   
206    // Iterate over all residues & add them to the tree
207  0 for (ChimeraResidue res : sortedResidues)
208    {
209  0 res.setDisplayType(this.residueDisplay);
210  0 residue = new DefaultMutableTreeNode(res);
211  0 residuePath = treePath.pathByAddingChild(residue);
212  0 res.setUserData(residuePath);
213  0 treeModel.add(residue);
214    }
215    }
216    }