Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ChimeraChain	47	57	34	0.00%	Show methods

Class ChimeraChain

Class ChimeraChain	Line # 47	Total Statements 57	Complexity 34	TOTAL Coverage 0.00%
ChimeraChain(int,int,String)   ChimeraChain(int,int,String)	9292	4.04	1.01	0.0 0.00%
setSelected(boolean) : void   setSelected(boolean) : void	106106	1.01	1.01	0.0 0.00%
isSelected() : boolean   isSelected() : boolean	116116	1.01	1.01	0.0 0.00%
hasSelectedChildren() : boolean   hasSelectedChildren() : boolean	121121	6.06	3.03	0.0 0.00%
getSelectedResidues() : List<ChimeraResidue>   getSelectedResidues() : List<ChimeraResidue>	143143	7.07	3.03	0.0 0.00%
addResidue(ChimeraResidue) : void   addResidue(ChimeraResidue) : void	167167	2.02	1.01	0.0 0.00%
getResidues() : Collection<ChimeraResidue>   getResidues() : Collection<ChimeraResidue>	179179	1.01	1.01	0.0 0.00%
getChildren() : List<ChimeraStructuralObject>   getChildren() : List<ChimeraStructuralObject>	189189	1.01	1.01	0.0 0.00%
getResidue(String) : ChimeraResidue   getResidue(String) : ChimeraResidue	201201	3.03	2.02	0.0 0.00%
getResidueRange(String) : List<ChimeraResidue>   getResidueRange(String) : List<ChimeraResidue>	216216	11.011	5.05	0.0 0.00%
getChainId() : String   getChainId() : String	240240	1.01	1.01	0.0 0.00%
getModelNumber() : int   getModelNumber() : int	250250	1.01	1.01	0.0 0.00%
getSubModelNumber() : int   getSubModelNumber() : int	260260	1.01	1.01	0.0 0.00%
displayName() : String   displayName() : String	271271	3.03	2.02	0.0 0.00%
toString() : String   toString() : String	289289	6.06	3.03	0.0 0.00%
toSpec() : String   toSpec() : String	311311	3.03	2.02	0.0 0.00%
getResidueCount() : int   getResidueCount() : int	328328	1.01	1.01	0.0 0.00%
setChimeraModel(ChimeraModel) : void   setChimeraModel(ChimeraModel) : void	339339	1.01	1.01	0.0 0.00%
getChimeraModel() : ChimeraModel   getChimeraModel() : ChimeraModel	349349	1.01	1.01	0.0 0.00%
getUserData() : Object   getUserData() : Object	359359	1.01	1.01	0.0 0.00%
setUserData(Object) : void   setUserData(Object) : void	370370	1.01	1.01	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		import java.util.ArrayList;
36		import java.util.Collection;
37		import java.util.List;
38		import java.util.TreeMap;
39
40		/**
41		* This class provides the implementation for the ChimeraChain object
42		*
43		* @author scooter
44		*
45		*/
46		// TODO: [Optional] Implement toAttr() method
		0% Uncovered Elements: 102 (102) Complexity: 34 Complexity Density: 0.6
47		public class ChimeraChain implements ChimeraStructuralObject
48		{
49
50		/**
51		* The model/subModel number this chain is a part of
52		*/
53		private int modelNumber;
54
55		private int subModelNumber;
56
57		/**
58		* A pointer to the model this chain is a part of
59		*/
60		private ChimeraModel chimeraModel;
61
62		/**
63		* The chainID (from the PDB record)
64		*/
65		private String chainId;
66
67		/**
68		* The residues that are part of this chain
69		*/
70		private TreeMap<String, ChimeraResidue> residueMap;
71
72		/**
73		* userData to associate with this chain
74		*/
75		private Object userData;
76
77		/**
78		* Flag to indicate the selection state
79		*/
80		private boolean selected = false;
81
82		/**
83		* Constructor to create a new ChimeraChain
84		*
85		* @param model
86		* the model number this chain is part of
87		* @param subModel
88		* the subModel number this chain is part of
89		* @param chainId
90		* the chain ID for this chain
91		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
92	0	public ChimeraChain(int model, int subModel, String chainId)...
93		{
94	0	this.modelNumber = model;
95	0	this.subModelNumber = subModel;
96	0	this.chainId = chainId;
97	0	residueMap = new TreeMap<String, ChimeraResidue>();
98		}
99
100		/**
101		* set the selected state of this chain
102		*
103		* @param selected
104		* a boolean to set the selected state to
105		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
106	0	public void setSelected(boolean selected)...
107		{
108	0	this.selected = selected;
109		}
110
111		/**
112		* return the selected state of this chain
113		*
114		* @return the selected state
115		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
116	0	public boolean isSelected()...
117		{
118	0	return selected;
119		}
120
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
121	0	public boolean hasSelectedChildren()...
122		{
123	0	if (selected)
124		{
125	0	return true;
126		}
127		else
128		{
129	0	for (ChimeraResidue residue : getResidues())
130		{
131	0	if (residue.isSelected())
132	0	return true;
133		}
134		}
135	0	return false;
136		}
137
138		/**
139		* Return the list of selected residues
140		*
141		* @return all selected residues
142		*/
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
143	0	public List<ChimeraResidue> getSelectedResidues()...
144		{
145	0	List<ChimeraResidue> residueList = new ArrayList<ChimeraResidue>();
146	0	if (selected)
147		{
148	0	residueList.addAll(getResidues());
149		}
150		else
151		{
152	0	for (ChimeraResidue residue : getResidues())
153		{
154	0	if (residue.isSelected())
155	0	residueList.add(residue);
156		}
157		}
158	0	return residueList;
159		}
160
161		/**
162		* Add a residue to the chain.
163		*
164		* @param residue
165		* the ChimeraResidue to add to the chain.
166		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
167	0	public void addResidue(ChimeraResidue residue)...
168		{
169	0	String index = residue.getIndex();
170		// Put it in our map so that we can return it in order
171	0	residueMap.put(index, residue);
172		}
173
174		/**
175		* Return the list of residues in this chain in pdb residue order
176		*
177		* @return a Collection of residues in residue order
178		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
179	0	public Collection<ChimeraResidue> getResidues()...
180		{
181	0	return residueMap.values();
182		}
183
184		/**
185		* Return the list of residues in this chain as a list
186		*
187		* @return List of residues
188		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
189	0	public List<ChimeraStructuralObject> getChildren()...
190		{
191	0	return new ArrayList<ChimeraStructuralObject>(residueMap.values());
192		}
193
194		/**
195		* Get a specific residue
196		*
197		* @param residueIndex
198		* String representation of the residue index
199		* @return the ChimeraResidue represented by the residueIndex
200		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
201	0	public ChimeraResidue getResidue(String index)...
202		{
203		// Integer index = Integer.valueOf(residueIndex);
204	0	if (residueMap.containsKey(index))
205	0	return residueMap.get(index);
206	0	return null;
207		}
208
209		/**
210		* Get a list of residues as a residue range
211		*
212		* @param residueRange
213		* String representation of the residue range
214		* @return the List of ChimeraResidues represented by the range
215		*/
		0% Uncovered Elements: 17 (17) Complexity: 5 Complexity Density: 0.45
216	0	public List<ChimeraResidue> getResidueRange(String residueRange)...
217		{
218	0	String[] range = residueRange.split("-", 2);
219	0	if (range[1] == null || range[1].length() == 0)
220		{
221	0	range[1] = range[0];
222		}
223	0	List<ChimeraResidue> resultRange = new ArrayList<ChimeraResidue>();
224	0	int start = Integer.parseInt(range[0]);
225	0	int end = Integer.parseInt(range[1]);
226	0	for (int i = start; i <= end; i++)
227		{
228	0	String index = String.valueOf(i);
229	0	if (residueMap.containsKey(index))
230	0	resultRange.add(residueMap.get(index));
231		}
232	0	return resultRange;
233		}
234
235		/**
236		* Get the ID for this chain
237		*
238		* @return String value of the chainId
239		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
240	0	public String getChainId()...
241		{
242	0	return chainId;
243		}
244
245		/**
246		* Get the model number for this chain
247		*
248		* @return the model number
249		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
250	0	public int getModelNumber()...
251		{
252	0	return modelNumber;
253		}
254
255		/**
256		* Get the sub-model number for this chain
257		*
258		* @return the sub-model number
259		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
260	0	public int getSubModelNumber()...
261		{
262	0	return subModelNumber;
263		}
264
265		/**
266		* Return a string representation of this chain as follows: Chain
267		* <i>chainId</i> (<i>residue_count</i> residues)
268		*
269		* @return String representation of chain
270		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
271	0	public String displayName()...
272		{
273	0	if (chainId.equals("_"))
274		{
275	0	return ("Chain (no ID) (" + getResidueCount() + " residues)");
276		}
277		else
278		{
279	0	return ("Chain " + chainId + " (" + getResidueCount() + " residues)");
280		}
281		}
282
283		/**
284		* Return a string representation of this chain as follows: Node xxx [Model
285		* yyyy Chain <i>chainId</i>]
286		*
287		* @return String representation of chain
288		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
289	0	public String toString()...
290		{
291	0	String displayName = chimeraModel.getModelName();
292	0	if (displayName.length() > 14)
293	0	displayName = displayName.substring(0, 13) + "...";
294	0	if (chainId.equals("_"))
295		{
296	0	return (displayName + " Chain (no ID) (" + getResidueCount()
297		+ " residues)");
298		}
299		else
300		{
301	0	return (displayName + " Chain " + chainId + " (" + getResidueCount()
302		+ " residues)");
303		}
304		}
305
306		/**
307		* Return the Chimera specification for this chain
308		*
309		* @return Chimera specification
310		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
311	0	public String toSpec()...
312		{
313	0	if (chainId.equals("_"))
314		{
315	0	return ("#" + modelNumber + "." + subModelNumber + ":.");
316		}
317		else
318		{
319	0	return ("#" + modelNumber + "." + subModelNumber + ":." + chainId);
320		}
321		}
322
323		/**
324		* Return the number of residues in this chain
325		*
326		* @return integer number of residues
327		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
328	0	public int getResidueCount()...
329		{
330	0	return residueMap.size();
331		}
332
333		/**
334		* Set the ChimeraModel for this chain
335		*
336		* @param model
337		* ChimeraModel to associate with this chain
338		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
339	0	public void setChimeraModel(ChimeraModel model)...
340		{
341	0	this.chimeraModel = model;
342		}
343
344		/**
345		* Get the ChimeraModel for this chain
346		*
347		* @return ChimeraModel associated with this chain
348		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
349	0	public ChimeraModel getChimeraModel()...
350		{
351	0	return chimeraModel;
352		}
353
354		/**
355		* Get the user data for this Chain
356		*
357		* @return user data
358		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
359	0	public Object getUserData()...
360		{
361	0	return userData;
362		}
363
364		/**
365		* Set the user data for this Chain
366		*
367		* @param data
368		* the user data to associate with this chain
369		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
370	0	public void setUserData(Object data)...
371		{
372	0	this.userData = data;
373		}
374		}