Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ChimeraResidue	49	74	39	0.00%	Show methods

Class ChimeraResidue

Class ChimeraResidue	Line # 49	Total Statements 74	Complexity 39	TOTAL Coverage 0.00%
ChimeraResidue(String,String,int)   ChimeraResidue(String,String,int)	9696	1.01	1.01	0.0 0.00%
ChimeraResidue(String,String,int,int)   ChimeraResidue(String,String,int,int)	113113	5.05	1.01	0.0 0.00%
ChimeraResidue(String)   ChimeraResidue(String)	135135	22.022	5.05	0.0 0.00%
setSelected(boolean) : void   setSelected(boolean) : void	192192	1.01	1.01	0.0 0.00%
isSelected() : boolean   isSelected() : boolean	202202	1.01	1.01	0.0 0.00%
getChildren() : List<ChimeraStructuralObject>   getChildren() : List<ChimeraStructuralObject>	213213	3.03	1.01	0.0 0.00%
displayName() : String   displayName() : String	228228	1.01	1.01	0.0 0.00%
toString() : String   toString() : String	241241	7.07	4.04	0.0 0.00%
toSpec() : String   toSpec() : String	266266	3.03	2.02	0.0 0.00%
getIndex() : String   getIndex() : String	279279	1.01	1.01	0.0 0.00%
getChainId() : String   getChainId() : String	289289	1.01	1.01	0.0 0.00%
getType() : String   getType() : String	299299	1.01	1.01	0.0 0.00%
getModelNumber() : int   getModelNumber() : int	309309	1.01	1.01	0.0 0.00%
getSubModelNumber() : int   getSubModelNumber() : int	319319	1.01	1.01	0.0 0.00%
getChimeraModel() : ChimeraModel   getChimeraModel() : ChimeraModel	329329	1.01	1.01	0.0 0.00%
setChimeraModel(ChimeraModel) : void   setChimeraModel(ChimeraModel) : void	340340	1.01	1.01	0.0 0.00%
getUserData() : Object   getUserData() : Object	350350	1.01	1.01	0.0 0.00%
setUserData(Object) : void   setUserData(Object) : void	361361	1.01	1.01	0.0 0.00%
compareTo(ChimeraResidue) : int   compareTo(ChimeraResidue) : int	366366	11.011	7.07	0.0 0.00%
splitInsertionCode(String) : void   splitInsertionCode(String) : void	383383	7.07	3.03	0.0 0.00%
setDisplayType(int) : void   setDisplayType(int) : void	444444	1.01	1.01	0.0 0.00%
getDisplayType() : int   getDisplayType() : int	449449	1.01	1.01	0.0 0.00%
hasSelectedChildren() : boolean   hasSelectedChildren() : boolean	454454	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.List;
37		import java.util.regex.Matcher;
38		import java.util.regex.Pattern;
39
40		import org.slf4j.LoggerFactory;
41
42		/**
43		* This class provides the implementation for the ChimeraResidue, object
44		*
45		* @author scooter
46		*
47		*/
48
		0% Uncovered Elements: 125 (125) Complexity: 39 Complexity Density: 0.53
49		public class ChimeraResidue
50		implements ChimeraStructuralObject, Comparable<ChimeraResidue>
51		{
52
53		/* Constants */
54		public static final int SINGLE_LETTER = 0; // Display residues as a single
55		// letter
56
57		public static final int THREE_LETTER = 1; // Display residues as three letters
58
59		public static final int FULL_NAME = 2; // Display full residue names
60
61		private String type; // Residue type
62
63		private String index; // Residue index
64
65		private String chainId; // ChainID for this residue
66
67		private int modelNumber; // model number for this residue
68
69		private int subModelNumber; // sub-model number for this residue
70
71		protected int residueNumber;
72
73		protected String insertionCode;
74
75		private ChimeraModel chimeraModel; // ChimeraModel the residue is part of
76
77		private Object userData; // user data to associate with this residue
78
79		// public static HashMap<String, String> aaNames = null; // a map of amino
80		// acid
81		// names
82		private static int displayType = THREE_LETTER; // the current display type
83
84		private boolean selected = false; // the selection state
85
86		/**
87		* Constructor to create a new ChimeraResidue
88		*
89		* @param type
90		* the residue type
91		* @param index
92		* the index of the residue
93		* @param modelNumber
94		* the model number this residue is part of
95		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
96	0	public ChimeraResidue(String type, String index, int modelNumber)...
97		{
98	0	this(type, index, modelNumber, 0);
99		}
100
101		/**
102		* Constructor to create a new ChimeraResidue
103		*
104		* @param type
105		* the residue type
106		* @param index
107		* the index of the residue
108		* @param modelNumber
109		* the model number this residue is part of
110		* @param subModelNumber
111		* the sub-model number this residue is part of
112		*/
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
113	0	public ChimeraResidue(String type, String index, int modelNumber,...
114		int subModelNumber)
115		{
116	0	this.type = type;
117	0	this.index = index;
118	0	this.modelNumber = modelNumber;
119	0	this.subModelNumber = subModelNumber;
120	0	splitInsertionCode(this.index);
121		// if (aaNames == null) {
122		// initNames();
123		// }
124		}
125
126		/**
127		* Constructor to create a new ChimeraResidue from an input line
128		*
129		* @param chimeraInputLine
130		* a Chimera residue description
131		*/
132		// invoked when listing (selected) residues: listr spec #0; lists level
133		// residue
134		// Line: residue id #0:37.A type MET
		0% Uncovered Elements: 28 (28) Complexity: 5 Complexity Density: 0.23
135	0	public ChimeraResidue(String chimeraInputLine)...
136		{
137		// initNames();
138	0	String[] split1 = chimeraInputLine.split(":");
139
140		// First half has model number -- get the number
141	0	int numberOffset = split1[0].indexOf('#');
142	0	String model = split1[0].substring(numberOffset + 1);
143	0	int decimalOffset = model.indexOf('.'); // Do we have a sub-model?
144	0	try
145		{
146	0	this.subModelNumber = 0;
147	0	if (decimalOffset > 0)
148		{
149	0	this.subModelNumber = Integer
150		.parseInt(model.substring(decimalOffset + 1));
151	0	this.modelNumber = Integer
152		.parseInt(model.substring(0, decimalOffset));
153		}
154		else
155		{
156	0	this.modelNumber = Integer.parseInt(model);
157		}
158		} catch (Exception e)
159		{
160	0	LoggerFactory.getLogger(ChimeraResidue.class)
161		.error("Unexpected return from Chimera: " + model);
162	0	this.modelNumber = -1;
163		}
164
165		// Second half has residue info: index & type
166	0	String[] rTokens = split1[1].split(" ");
167	0	this.type = rTokens[2];
168
169	0	String[] iTokens = rTokens[0].split("\\.");
170	0	if (iTokens.length > 0)
171		{
172	0	this.index = iTokens[0];
173
174		// Careful, might or might not have a chainID
175	0	if (iTokens.length > 1)
176	0	this.chainId = iTokens[1];
177		else
178	0	this.chainId = "_";
179		}
180		else
181	0	this.index = rTokens[0];
182
183	0	splitInsertionCode(this.index);
184		}
185
186		/**
187		* Set the selected state for this residue
188		*
189		* @param selected
190		* the selection state to set
191		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
192	0	public void setSelected(boolean selected)...
193		{
194	0	this.selected = selected;
195		}
196
197		/**
198		* Return the selected state of this residue
199		*
200		* @return the selected state
201		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
202	0	public boolean isSelected()...
203		{
204	0	return selected;
205		}
206
207		/**
208		* Return an array made up of this residue (required for
209		* ChimeraStructuralObject interface
210		*
211		* @return a List with this residue as its sole member
212		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
213	0	public List<ChimeraStructuralObject> getChildren()...
214		{
215	0	List<ChimeraStructuralObject> v = new ArrayList<ChimeraStructuralObject>();
216	0	v.add(this);
217	0	return v;
218		}
219
220		/**
221		* Return the string representation of this residue as follows:
222		* "<i>residue_name</i> <i>index</i>" where <i>residue_name</i> could be
223		* either the single letter, three letter, or full name representation of the
224		* amino acid.
225		*
226		* @return the string representation
227		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
228	0	public String displayName()...
229		{
230	0	return toString();
231		}
232
233		/**
234		* Return the string representation of this residue as follows:
235		* "<i>residue_name</i> <i>index</i>" where <i>residue_name</i> could be
236		* either the single letter, three letter, or full name representation of the
237		* amino acid.
238		*
239		* @return the string representation
240		*/
		0% Uncovered Elements: 13 (13) Complexity: 4 Complexity Density: 0.57
241	0	public String toString()...
242		{
243	0	if (displayType == FULL_NAME)
244		{
245	0	return (ChimUtils.toFullName(type) + " " + index);
246		}
247	0	else if (displayType == SINGLE_LETTER)
248		{
249	0	return (ChimUtils.toSingleLetter(type) + " " + index);
250		}
251	0	else if (displayType == THREE_LETTER)
252		{
253	0	return (ChimUtils.toThreeLetter(type) + " " + index);
254		}
255		else
256		{
257	0	return (type + " " + index);
258		}
259		}
260
261		/**
262		* Return the Chimera specification for this Residue
263		*
264		* @return Chimera specification
265		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
266	0	public String toSpec()...
267		{
268	0	if (!chainId.equals("_"))
269	0	return ("#" + modelNumber + ":" + index + "." + chainId);
270		else
271	0	return ("#" + modelNumber + ":" + index + ".");
272		}
273
274		/**
275		* Get the index of this residue
276		*
277		* @return residue index
278		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
279	0	public String getIndex()...
280		{
281	0	return this.index;
282		}
283
284		/**
285		* Get the chainID for this residue
286		*
287		* @return String value of the chainId
288		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
289	0	public String getChainId()...
290		{
291	0	return this.chainId;
292		}
293
294		/**
295		* Get the type for this residue
296		*
297		* @return residue type
298		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
299	0	public String getType()...
300		{
301	0	return this.type;
302		}
303
304		/**
305		* Get the model number for this residue
306		*
307		* @return the model number
308		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
309	0	public int getModelNumber()...
310		{
311	0	return this.modelNumber;
312		}
313
314		/**
315		* Get the sub-model number for this residue
316		*
317		* @return the sub-model number
318		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
319	0	public int getSubModelNumber()...
320		{
321	0	return this.subModelNumber;
322		}
323
324		/**
325		* Get the model this residue is part of
326		*
327		* @return the ChimeraModel
328		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
329	0	public ChimeraModel getChimeraModel()...
330		{
331	0	return this.chimeraModel;
332		}
333
334		/**
335		* Set the model this residue is part of
336		*
337		* @param chimeraModel
338		* the ChimeraModel this model is part of
339		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
340	0	public void setChimeraModel(ChimeraModel chimeraModel)...
341		{
342	0	this.chimeraModel = chimeraModel;
343		}
344
345		/**
346		* Get the user data for this residue
347		*
348		* @return user data
349		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
350	0	public Object getUserData()...
351		{
352	0	return userData;
353		}
354
355		/**
356		* Set the user data for this Residue
357		*
358		* @param data
359		* the user data to associate with this residue
360		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
361	0	public void setUserData(Object data)...
362		{
363	0	this.userData = data;
364		}
365
		0% Uncovered Elements: 21 (21) Complexity: 7 Complexity Density: 0.64
366	0	public int compareTo(ChimeraResidue c2)...
367		{
368	0	if (residueNumber < c2.residueNumber)
369	0	return -1;
370	0	else if (residueNumber == c2.residueNumber)
371		{
372	0	if (insertionCode == null && c2.insertionCode == null)
373	0	return 0;
374	0	else if (insertionCode == null)
375	0	return -1;
376	0	else if (c2.insertionCode == null)
377	0	return 1;
378	0	return (insertionCode.compareTo(c2.insertionCode));
379		}
380	0	return 1;
381		}
382
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
383	0	public void splitInsertionCode(String residue)...
384		{
385		// OK, split the index into number and insertion code
386		// JBPNote - m.matches() can be true even if there is no resnum - this can
387		// cause NumberFormatExceptions below
388	0	Pattern p = Pattern.compile("(\\d*)([A-Z]?)");
389	0	Matcher m = p.matcher(residue);
390	0	if (m.matches())
391		{
392	0	this.residueNumber = Integer.parseInt(m.group(1));
393	0	if (m.groupCount() > 1)
394	0	this.insertionCode = m.group(2);
395		else
396	0	this.insertionCode = null;
397		}
398		}
399
400		/**********************************************
401		* Static routines
402		*********************************************/
403
404		/**
405		* Initialize the residue names
406		*/
407		// private static void initNames() {
408		// // Create our residue name table
409		// aaNames = new HashMap<String, String>();
410		// aaNames.put("ALA", "A Ala Alanine N[C@@H](C)C(O)=O");
411		// aaNames.put("ARG", "R Arg Arginine N[C@@H](CCCNC(N)=N)C(O)=O");
412		// aaNames.put("ASN", "N Asn Asparagine N[C@@H](CC(N)=O)C(O)=O");
413		// aaNames.put("ASP", "D Asp Aspartic_acid N[C@@H](CC(O)=O)C(O)=O");
414		// aaNames.put("CYS", "C Cys Cysteine N[C@@H](CS)C(O)=O");
415		// aaNames.put("GLN", "Q Gln Glutamine N[C@H](C(O)=O)CCC(N)=O");
416		// aaNames.put("GLU", "E Glu Glumatic_acid N[C@H](C(O)=O)CCC(O)=O");
417		// aaNames.put("GLY", "G Gly Glycine NCC(O)=O");
418		// aaNames.put("HIS", "H His Histidine N[C@@H](CC1=CN=CN1)C(O)=O");
419		// aaNames.put("ILE", "I Ile Isoleucine N[C@]([C@H](C)CC)([H])C(O)=O");
420		// aaNames.put("LEU", "L Leu Leucine N[C@](CC(C)C)([H])C(O)=O");
421		// aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
422		// aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
423		// aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
424		// aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
425		// aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
426		// aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
427		// aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
428		// aaNames.put("TRP",
429		// "W Trp Tryptophan N[C@@]([H])(CC1=CN([H])C2=C1C=CC=C2)C(O)=O");
430		// aaNames.put("TYR", "Y Tyr Tyrosine N[C@@](C(O)=O)([H])CC1=CC=C(O)C=C1");
431		// aaNames.put("VAL", "V Val Valine N[C@@](C(O)=O)([H])C(C)C");
432		// aaNames.put("ASX", "B Asx Aspartic_acid_or_Asparagine");
433		// aaNames.put("GLX", "Z Glx Glutamine_or_Glutamic_acid");
434		// aaNames.put("XAA", "X Xaa Any_or_unknown_amino_acid");
435		// aaNames.put("HOH", "HOH HOH Water [H]O[H]");
436		// }
437
438		/**
439		* Set the display type.
440		*
441		* @param type
442		* the display type
443		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
444	0	public static void setDisplayType(int type)...
445		{
446	0	displayType = type;
447		}
448
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
449	0	public static int getDisplayType()...
450		{
451	0	return displayType;
452		}
453
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
454	0	public boolean hasSelectedChildren()...
455		{
456	0	return false;
457		}
458		}