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Coverage Report

  1. Project Clover database Wed Nov 6 2024 14:47:21 GMT
  2. Package ext.edu.ucsf.rbvi.strucviz2

File ChimeraModel.java

 

Coverage histogram

../../../../../img/srcFileCovDistChart0.png
59% of files have more coverage

Code metrics

48
130
35
1
623
360
59
0.45
3.71
35
1.69

Classes

Class Line # Actions
ChimeraModel 52 130 59
0.00%
 

Contributing tests

No tests hitting this source file were found.

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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    */
 
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    */
 
86  0 toggle 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
 
107  0 toggle 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    */
 
132  0 toggle 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    */
 
158  0 toggle 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    */
 
180  0 toggle @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    */
 
191  0 toggle 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    */
 
202  0 toggle 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    */
 
212  0 toggle 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    */
 
223  0 toggle 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    */
 
233  0 toggle 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    */
 
244  0 toggle 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    */
 
254  0 toggle 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    */
 
265  0 toggle public void setSubModelNumber(int subModelNumber)
266    {
267  0 this.subModelNumber = subModelNumber;
268    }
269   
 
270  0 toggle public ModelType getModelType()
271    {
272  0 return type;
273    }
274   
 
275  0 toggle public void setModelType(ModelType type)
276    {
277  0 this.type = type;
278    }
279   
 
280  0 toggle public HashSet<ChimeraResidue> getFuncResidues()
281    {
282  0 return funcResidues;
283    }
284   
 
285  0 toggle 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    */
 
308  0 toggle @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    */
 
320  0 toggle @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    */
 
331  0 toggle @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    */
 
343  0 toggle @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    */
 
354  0 toggle @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    */
 
365  0 toggle 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    */
 
375  0 toggle 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    */
 
385  0 toggle 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    */
 
395  0 toggle 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    */
 
410  0 toggle 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    */
 
427  0 toggle 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    */
 
443  0 toggle 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    */
 
455  0 toggle @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    */
 
480  0 toggle 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    */
 
500  0 toggle @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    */
 
514  0 toggle @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   
 
601  0 toggle @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   
 
614  0 toggle @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    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 6 2024 14:54:51 GMT using coverage data from Wed Nov 6 2024 14:54:40 GMT.
  • OpenClover is free and open-source software.