Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ChimeraTreeModel	55	47	8	56	0.00%	Show methods

Class ChimeraTreeModel

Class ChimeraTreeModel	Line # 55	Total Statements 47	Complexity 8	Uncovered Elements 56	TOTAL Coverage 0.00%
ChimeraTreeModel(ChimeraManager,JTree)   ChimeraTreeModel(ChimeraManager,JTree)	7272	5.05	1.01	5.05	0.0 0.00%
setResidueDisplay(int) : void   setResidueDisplay(int) : void	9191	1.01	1.01	1.01	0.0 0.00%
reload() : void   reload() : void	9999	3.03	1.01	3.03	0.0 0.00%
rebuildTree() : void   rebuildTree() : void	112112	4.04	1.01	4.04	0.0 0.00%
buildTree() : DefaultMutableTreeNode   buildTree() : DefaultMutableTreeNode	126126	12.012	1.01	12.012	0.0 0.00%
addChainNodes(ChimeraModel,DefaultMutableTreeNode,TreePath) : void   addChainNodes(ChimeraModel,DefaultMutableTreeNode,TreePath) : void	158158	12.012	2.02	14.014	0.0 0.00%
addResidues(Collection<ChimeraResidue>,DefaultMutableTreeNode,TreePath) : void   addResidues(Collection<ChimeraResidue>,DefaultMutableTreeNode,TreePath) : void	196196	10.010	1.01	10.010	0.0 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		*/
		0% Uncovered Elements: 56 (56) Complexity: 8 Complexity Density: 0.17
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		*/
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
72	0	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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
91	0	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		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
99	0	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		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
112	0	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		*/
		0% Uncovered Elements: 12 (12) Complexity: 1 Complexity Density: 0.08
126	0	private DefaultMutableTreeNode buildTree()...
127		{
128	0	int modelCount = chimeraManager.getChimeraModelsCount(true);
129	0	DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(modelCount
130		+ " 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		*/
		0% Uncovered Elements: 14 (14) Complexity: 2 Complexity Density: 0.17
158	0	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		*/
		0% Uncovered Elements: 10 (10) Complexity: 1 Complexity Density: 0.1
196	0	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		}