Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ChimeraModel	52	130	59	213	0.00%	Show methods

Class ChimeraModel

Class ChimeraModel	Line # 52	Total Statements 130	Complexity 59	Uncovered Elements 213	TOTAL Coverage 0.00%
ChimeraModel(String,ModelType,int,int)   ChimeraModel(String,ModelType,int,int)	8686	6.06	1.01	6.06	0.0 0.00%
ChimeraModel(String)   ChimeraModel(String)	107107	8.08	2.02	10.010	0.0 0.00%
addResidue(ChimeraResidue) : void   addResidue(ChimeraResidue) : void	132132	5.05	2.02	7.07	0.0 0.00%
addResidue(String,ChimeraResidue) : void   addResidue(String,ChimeraResidue) : void	158158	7.07	2.02	9.09	0.0 0.00%
getChimeraModel() : ChimeraModel   getChimeraModel() : ChimeraModel	180180	1.01	1.01	1.01	0.0 0.00%
getModelColor() : Color   getModelColor() : Color	191191	1.01	1.01	1.01	0.0 0.00%
setModelColor(Color) : void   setModelColor(Color) : void	202202	1.01	1.01	1.01	0.0 0.00%
getModelName() : String   getModelName() : String	212212	1.01	1.01	1.01	0.0 0.00%
setModelName(String) : void   setModelName(String) : void	223223	1.01	1.01	1.01	0.0 0.00%
getModelNumber() : int   getModelNumber() : int	233233	1.01	1.01	1.01	0.0 0.00%
setModelNumber(int) : void   setModelNumber(int) : void	244244	1.01	1.01	1.01	0.0 0.00%
getSubModelNumber() : int   getSubModelNumber() : int	254254	1.01	1.01	1.01	0.0 0.00%
setSubModelNumber(int) : void   setSubModelNumber(int) : void	265265	1.01	1.01	1.01	0.0 0.00%
getModelType() : ModelType   getModelType() : ModelType	270270	1.01	1.01	1.01	0.0 0.00%
setModelType(ModelType) : void   setModelType(ModelType) : void	275275	1.01	1.01	1.01	0.0 0.00%
getFuncResidues() : HashSet<ChimeraResidue>   getFuncResidues() : HashSet<ChimeraResidue>	280280	1.01	1.01	1.01	0.0 0.00%
setFuncResidues(List<String>) : void   setFuncResidues(List<String>) : void	285285	5.05	2.02	7.07	0.0 0.00%
getUserData() : Object   getUserData() : Object	308308	1.01	1.01	1.01	0.0 0.00%
setUserData(Object) : void   setUserData(Object) : void	320320	1.01	1.01	1.01	0.0 0.00%
isSelected() : boolean   isSelected() : boolean	331331	1.01	1.01	1.01	0.0 0.00%
setSelected(boolean) : void   setSelected(boolean) : void	343343	1.01	1.01	1.01	0.0 0.00%
getChildren() : List<ChimeraStructuralObject>   getChildren() : List<ChimeraStructuralObject>	354354	1.01	1.01	1.01	0.0 0.00%
getChains() : Collection<ChimeraChain>   getChains() : Collection<ChimeraChain>	365365	1.01	1.01	1.01	0.0 0.00%
getChainCount() : int   getChainCount() : int	375375	1.01	1.01	1.01	0.0 0.00%
getChainNames() : Collection<String>   getChainNames() : Collection<String>	385385	1.01	1.01	1.01	0.0 0.00%
getResidues() : Collection<ChimeraResidue>   getResidues() : Collection<ChimeraResidue>	395395	4.04	1.01	4.04	0.0 0.00%
getResidueCount() : int   getResidueCount() : int	410410	4.04	1.01	4.04	0.0 0.00%
getChain(String) : ChimeraChain   getChain(String) : ChimeraChain	427427	3.03	2.02	5.05	0.0 0.00%
getResidue(String,String) : ChimeraResidue   getResidue(String,String) : ChimeraResidue	443443	3.03	2.02	5.05	0.0 0.00%
hasSelectedChildren() : boolean   hasSelectedChildren() : boolean	455455	6.06	3.03	10.010	0.0 0.00%
getSelectedResidues() : List<ChimeraResidue>   getSelectedResidues() : List<ChimeraResidue>	480480	6.06	2.02	8.08	0.0 0.00%
toSpec() : String   toSpec() : String	500500	3.03	2.02	5.05	0.0 0.00%
toString() : String   toString() : String	514514	41.041	14.014	67.067	0.0 0.00%
equals(Object) : boolean   equals(Object) : boolean	601601	4.04	2.02	6.06	0.0 0.00%
hashCode() : int   hashCode() : int	614614	5.05	1.01	5.05	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.awt.Color;
36		import java.util.ArrayList;
37		import java.util.Collection;
38		import java.util.HashSet;
39		import java.util.List;
40		import java.util.Set;
41		import java.util.TreeMap;
42
43		import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
44
45		/**
46		* This class provides the implementation for the ChimeraModel, ChimeraChain,
47		* and ChimeraResidue objects
48		*
49		* @author scooter
50		*
51		*/
		0% Uncovered Elements: 213 (213) Complexity: 59 Complexity Density: 0.45
52		public class ChimeraModel implements ChimeraStructuralObject
53		{
54
55		private String name; // The name of this model
56
57		private ModelType type; // The type of the model
58
59		private int modelNumber; // The model number
60
61		private int subModelNumber; // The sub-model number
62
63		private Color modelColor = null; // The color of this model (from Chimera)
64
65		private Object userData = null; // User data associated with this model
66
67		private boolean selected = false; // The selected state of this model
68
69		private TreeMap<String, ChimeraChain> chainMap; // The list of chains
70
71		// private TreeMap<String, ChimeraResidue> residueMap; // The list of residues
72		private HashSet<ChimeraResidue> funcResidues; // List of functional residues
73
74		/**
75		* Constructor to create a model
76		*
77		* @param name
78		* the name of this model
79		* @param color
80		* the model Color
81		* @param modelNumber
82		* the model number
83		* @param subModelNumber
84		* the sub-model number
85		*/
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
86	0	public ChimeraModel(String name, ModelType type, int modelNumber,...
87		int subModelNumber)
88		{
89	0	this.name = name;
90	0	this.type = type;
91	0	this.modelNumber = modelNumber;
92	0	this.subModelNumber = subModelNumber;
93
94	0	this.chainMap = new TreeMap<String, ChimeraChain>();
95	0	this.funcResidues = new HashSet<ChimeraResidue>();
96		}
97
98		/**
99		* Constructor to create a model from the Chimera input line
100		*
101		* @param inputLine
102		* Chimera input line from which to construct this model
103		*/
104		// TODO: [Optional] How to distinguish between PDB and MODBASE?
105		// invoked when listing models: listm type molecule; lists level molecule
106		// line = model id #0 type Molecule name 1ert
		0% Uncovered Elements: 10 (10) Complexity: 2 Complexity Density: 0.25
107	0	public ChimeraModel(String inputLine)...
108		{
109	0	this.name = ChimUtils.parseModelName(inputLine);
110		// TODO: [Optional] Write a separate method to get model type
111	0	if (name.startsWith("smiles"))
112		{
113	0	this.type = ModelType.SMILES;
114		}
115		else
116		{
117	0	this.type = ModelType.PDB_MODEL;
118		}
119	0	this.modelNumber = ChimUtils.parseModelNumber(inputLine)[0];
120	0	this.subModelNumber = ChimUtils.parseModelNumber(inputLine)[1];
121
122	0	this.chainMap = new TreeMap<String, ChimeraChain>();
123	0	this.funcResidues = new HashSet<ChimeraResidue>();
124		}
125
126		/**
127		* Add a residue to this model
128		*
129		* @param residue
130		* to add to the model
131		*/
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
132	0	public void addResidue(ChimeraResidue residue)...
133		{
134	0	residue.setChimeraModel(this);
135		// residueMap.put(residue.getIndex(), residue);
136	0	String chainId = residue.getChainId();
137	0	if (chainId != null)
138		{
139	0	addResidue(chainId, residue);
140		}
141		else
142		{
143	0	addResidue("_", residue);
144		}
145		// Put it in our map so that we can return it in order
146		// residueMap.put(residue.getIndex(), residue);
147		}
148
149		/**
150		* Add a residue to a chain in this model. If the chain associated with
151		* chainId doesn't exist, it will be created.
152		*
153		* @param chainId
154		* to add the residue to
155		* @param residue
156		* to add to the chain
157		*/
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
158	0	public void addResidue(String chainId, ChimeraResidue residue)...
159		{
160	0	ChimeraChain chain = null;
161	0	if (!chainMap.containsKey(chainId))
162		{
163	0	chain = new ChimeraChain(this.modelNumber, this.subModelNumber,
164		chainId);
165	0	chain.setChimeraModel(this);
166	0	chainMap.put(chainId, chain);
167		}
168		else
169		{
170	0	chain = chainMap.get(chainId);
171		}
172	0	chain.addResidue(residue);
173		}
174
175		/**
176		* Get the ChimeraModel (required for ChimeraStructuralObject interface)
177		*
178		* @return ChimeraModel
179		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
180	0	@Override...
181		public ChimeraModel getChimeraModel()
182		{
183	0	return this;
184		}
185
186		/**
187		* Get the model color of this model
188		*
189		* @return model color of this model
190		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
191	0	public Color getModelColor()...
192		{
193	0	return this.modelColor;
194		}
195
196		/**
197		* Set the color of this model
198		*
199		* @param color
200		* Color of this model
201		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
202	0	public void setModelColor(Color color)...
203		{
204	0	this.modelColor = color;
205		}
206
207		/**
208		* Return the name of this model
209		*
210		* @return model name
211		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
212	0	public String getModelName()...
213		{
214	0	return name;
215		}
216
217		/**
218		* Set the name of this model
219		*
220		* @param name
221		* model name
222		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
223	0	public void setModelName(String name)...
224		{
225	0	this.name = name;
226		}
227
228		/**
229		* Get the model number of this model
230		*
231		* @return integer model number
232		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
233	0	public int getModelNumber()...
234		{
235	0	return modelNumber;
236		}
237
238		/**
239		* Set the model number of this model
240		*
241		* @param modelNumber
242		* integer model number
243		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
244	0	public void setModelNumber(int modelNumber)...
245		{
246	0	this.modelNumber = modelNumber;
247		}
248
249		/**
250		* Get the sub-model number of this model
251		*
252		* @return integer sub-model number
253		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
254	0	public int getSubModelNumber()...
255		{
256	0	return subModelNumber;
257		}
258
259		/**
260		* Set the sub-model number of this model
261		*
262		* @param subModelNumber
263		* integer model number
264		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
265	0	public void setSubModelNumber(int subModelNumber)...
266		{
267	0	this.subModelNumber = subModelNumber;
268		}
269
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
270	0	public ModelType getModelType()...
271		{
272	0	return type;
273		}
274
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
275	0	public void setModelType(ModelType type)...
276		{
277	0	this.type = type;
278		}
279
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
280	0	public HashSet<ChimeraResidue> getFuncResidues()...
281		{
282	0	return funcResidues;
283		}
284
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
285	0	public void setFuncResidues(List<String> residues)...
286		{
287	0	for (String residue : residues)
288		{
289	0	for (ChimeraChain chain : getChains())
290		{
291	0	if (residue.indexOf("-") > 0)
292		{
293	0	funcResidues.addAll(chain.getResidueRange(residue));
294		}
295		else
296		{
297	0	funcResidues.add(chain.getResidue(residue));
298		}
299		}
300		}
301		}
302
303		/**
304		* Get the user data for this model
305		*
306		* @return user data
307		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
308	0	@Override...
309		public Object getUserData()
310		{
311	0	return userData;
312		}
313
314		/**
315		* Set the user data for this model
316		*
317		* @param data
318		* user data to associate with this model
319		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
320	0	@Override...
321		public void setUserData(Object data)
322		{
323	0	this.userData = data;
324		}
325
326		/**
327		* Return the selected state of this model
328		*
329		* @return the selected state
330		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
331	0	@Override...
332		public boolean isSelected()
333		{
334	0	return selected;
335		}
336
337		/**
338		* Set the selected state of this model
339		*
340		* @param selected
341		* a boolean to set the selected state to
342		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
343	0	@Override...
344		public void setSelected(boolean selected)
345		{
346	0	this.selected = selected;
347		}
348
349		/**
350		* Return the chains in this model as a List
351		*
352		* @return the chains in this model as a list
353		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
354	0	@Override...
355		public List<ChimeraStructuralObject> getChildren()
356		{
357	0	return new ArrayList<ChimeraStructuralObject>(chainMap.values());
358		}
359
360		/**
361		* Return the chains in this model as a colleciton
362		*
363		* @return the chains in this model
364		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
365	0	public Collection<ChimeraChain> getChains()...
366		{
367	0	return chainMap.values();
368		}
369
370		/**
371		* Get the number of chains in this model
372		*
373		* @return integer chain count
374		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
375	0	public int getChainCount()...
376		{
377	0	return chainMap.size();
378		}
379
380		/**
381		* Get the list of chain names associated with this model
382		*
383		* @return return the list of chain names for this model
384		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
385	0	public Collection<String> getChainNames()...
386		{
387	0	return chainMap.keySet();
388		}
389
390		/**
391		* Get the residues associated with this model
392		*
393		* @return the list of residues in this model
394		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
395	0	public Collection<ChimeraResidue> getResidues()...
396		{
397	0	Collection<ChimeraResidue> residues = new ArrayList<ChimeraResidue>();
398	0	for (ChimeraChain chain : getChains())
399		{
400	0	residues.addAll(chain.getResidues());
401		}
402	0	return residues;
403		}
404
405		/**
406		* Get the number of residues in this model
407		*
408		* @return integer residues count
409		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
410	0	public int getResidueCount()...
411		{
412	0	int count = 0;
413	0	for (ChimeraChain chain : getChains())
414		{
415	0	count += chain.getResidueCount();
416		}
417	0	return count;
418		}
419
420		/**
421		* Get a specific chain from the model
422		*
423		* @param chain
424		* the ID of the chain to return
425		* @return ChimeraChain associated with the chain
426		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
427	0	public ChimeraChain getChain(String chain)...
428		{
429	0	if (chainMap.containsKey(chain))
430		{
431	0	return chainMap.get(chain);
432		}
433	0	return null;
434		}
435
436		/**
437		* Return a specific residue based on its index
438		*
439		* @param index
440		* of the residue to return
441		* @return the residue associated with that index
442		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
443	0	public ChimeraResidue getResidue(String chainId, String index)...
444		{
445	0	if (chainMap.containsKey(chainId))
446		{
447	0	return chainMap.get(chainId).getResidue(index);
448		}
449	0	return null;
450		}
451
452		/**
453		* Checks if this model has selected children.
454		*/
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
455	0	@Override...
456		public boolean hasSelectedChildren()
457		{
458	0	if (selected)
459		{
460	0	return true;
461		}
462		else
463		{
464	0	for (ChimeraChain chain : getChains())
465		{
466	0	if (chain.hasSelectedChildren())
467		{
468	0	return true;
469		}
470		}
471		}
472	0	return false;
473		}
474
475		/**
476		* Return the list of selected residues
477		*
478		* @return all selected residues
479		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
480	0	public List<ChimeraResidue> getSelectedResidues()...
481		{
482	0	List<ChimeraResidue> residueList = new ArrayList<ChimeraResidue>();
483	0	for (ChimeraChain chain : getChains())
484		{
485	0	if (selected)
486		{
487	0	residueList.addAll(chain.getSelectedResidues());
488		}
489		else
490		{
491	0	residueList.addAll(getResidues());
492		}
493		}
494	0	return residueList;
495		}
496
497		/**
498		* Return the Chimera specification for this model.
499		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
500	0	@Override...
501		public String toSpec()
502		{
503	0	if (subModelNumber == 0)
504		{
505	0	return ("#" + modelNumber);
506		}
507	0	return ("#" + modelNumber + "." + subModelNumber);
508		}
509
510		/**
511		* Return a string representation for the model. Shorten if longer than 100
512		* characters.
513		*/
		0% Uncovered Elements: 67 (67) Complexity: 14 Complexity Density: 0.34
514	0	@Override...
515		public String toString()
516		{
517	0	String modelName = "";
518		// TODO: [Optional] Change cutoff for shortening model names in the
519		// structure naviagator dialog
520	0	if (getChainCount() > 0)
521		{
522	0	modelName = "Model " + toSpec() + " " + name + " (" + getChainCount()
523		+ " chains, " + getResidueCount() + " residues)";
524		}
525	0	else if (getResidueCount() > 0)
526		{
527	0	modelName = "Model " + toSpec() + " " + name + " ("
528		+ getResidueCount() + " residues)";
529		}
530		else
531		{
532	0	modelName = "Model " + toSpec() + " " + name + "";
533		}
534
535	0	Set<String> networkNames = new HashSet<String>();
536	0	Set<String> nodeNames = new HashSet<String>();
537	0	Set<String> edgeNames = new HashSet<String>();
538
539	0	String cytoName = " [";
540	0	if (networkNames.size() > 0)
541		{
542	0	if (networkNames.size() == 1)
543		{
544	0	cytoName += "Network {";
545		}
546	0	else if (networkNames.size() > 1)
547		{
548	0	cytoName += "Networks {";
549		}
550	0	for (String cName : networkNames)
551		{
552	0	cytoName += cName + ",";
553		}
554	0	cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
555		}
556	0	if (nodeNames.size() > 0)
557		{
558	0	if (nodeNames.size() == 1)
559		{
560	0	cytoName += "Node {";
561		}
562	0	else if (nodeNames.size() > 1)
563		{
564	0	cytoName += "Nodes {";
565		}
566	0	for (String cName : nodeNames)
567		{
568	0	cytoName += cName + ",";
569		}
570	0	cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
571		}
572	0	if (edgeNames.size() > 0)
573		{
574	0	if (edgeNames.size() == 1)
575		{
576	0	cytoName += "Edge {";
577		}
578	0	else if (edgeNames.size() > 1)
579		{
580	0	cytoName += "Edges {";
581		}
582	0	for (String cName : edgeNames)
583		{
584	0	cytoName += cName + ",";
585		}
586	0	cytoName = cytoName.substring(0, cytoName.length() - 1) + "}, ";
587		}
588	0	if (cytoName.endsWith(", "))
589		{
590	0	cytoName = cytoName.substring(0, cytoName.length() - 2);
591		}
592	0	cytoName += "]";
593	0	String nodeName = modelName + cytoName;
594	0	if (nodeName.length() > 100)
595		{
596	0	nodeName = nodeName.substring(0, 100) + "...";
597		}
598	0	return nodeName;
599		}
600
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
601	0	@Override...
602		public boolean equals(Object otherChimeraModel)
603		{
604	0	if (!(otherChimeraModel instanceof ChimeraModel))
605		{
606	0	return false;
607		}
608	0	ChimeraModel otherCM = ((ChimeraModel) otherChimeraModel);
609	0	return this.name.equals(otherCM.name)
610		&& this.modelNumber == otherCM.modelNumber
611		&& this.type == otherCM.type;
612		}
613
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
614	0	@Override...
615		public int hashCode()
616		{
617	0	int hashCode = 1;
618	0	hashCode = hashCode * 37 + this.name.hashCode();
619	0	hashCode = hashCode * 37 + this.type.hashCode();
620	0	hashCode = (hashCode * 37) + modelNumber;
621	0	return hashCode;
622		}
623		}