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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.ext.rbvi.chimera

File ChimeraCommands.java

 

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../../../../img/srcFileCovDistChart6.png
35% of files have more coverage

Code metrics

66
149
10
1
546
321
52
0.35
14.9
10
5.2

Classes

Class Line # Actions
ChimeraCommands 51 149 52 110
0.5111111451.1%
 

Contributing tests

This file is covered by 4 tests. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.ext.rbvi.chimera;
22   
23    import jalview.api.AlignViewportI;
24    import jalview.api.AlignmentViewPanel;
25    import jalview.api.FeatureRenderer;
26    import jalview.api.SequenceRenderer;
27    import jalview.datamodel.AlignmentI;
28    import jalview.datamodel.HiddenColumns;
29    import jalview.datamodel.SequenceFeature;
30    import jalview.datamodel.SequenceI;
31    import jalview.renderer.seqfeatures.FeatureColourFinder;
32    import jalview.structure.StructureMapping;
33    import jalview.structure.StructureMappingcommandSet;
34    import jalview.structure.StructureSelectionManager;
35    import jalview.util.ColorUtils;
36    import jalview.util.Comparison;
37   
38    import java.awt.Color;
39    import java.util.ArrayList;
40    import java.util.HashMap;
41    import java.util.LinkedHashMap;
42    import java.util.List;
43    import java.util.Map;
44   
45    /**
46    * Routines for generating Chimera commands for Jalview/Chimera binding
47    *
48    * @author JimP
49    *
50    */
 
51    public class ChimeraCommands
52    {
53   
54    public static final String NAMESPACE_PREFIX = "jv_";
55   
56    /**
57    * Constructs Chimera commands to colour residues as per the Jalview alignment
58    *
59    * @param ssm
60    * @param files
61    * @param sequence
62    * @param sr
63    * @param fr
64    * @param viewPanel
65    * @return
66    */
 
67  1 toggle public static StructureMappingcommandSet[] getColourBySequenceCommand(
68    StructureSelectionManager ssm, String[] files,
69    SequenceI[][] sequence, SequenceRenderer sr,
70    AlignmentViewPanel viewPanel)
71    {
72  1 Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
73    sequence, sr, viewPanel);
74   
75  1 List<String> colourCommands = buildColourCommands(colourMap);
76   
77  1 StructureMappingcommandSet cs = new StructureMappingcommandSet(
78    ChimeraCommands.class, null,
79    colourCommands.toArray(new String[colourCommands.size()]));
80   
81  1 return new StructureMappingcommandSet[] { cs };
82    }
83   
84    /**
85    * Traverse the map of colours/models/chains/positions to construct a list of
86    * 'color' commands (one per distinct colour used). The format of each command
87    * is
88    *
89    * <pre>
90    * <blockquote>
91    * color colorname #modelnumber:range.chain
92    * e.g. color #00ff00 #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
93    * </blockquote>
94    * </pre>
95    *
96    * @param colourMap
97    * @return
98    */
 
99  2 toggle protected static List<String> buildColourCommands(
100    Map<Object, AtomSpecModel> colourMap)
101    {
102    /*
103    * This version concatenates all commands into a single String (semi-colon
104    * delimited). If length limit issues arise, refactor to return one color
105    * command per colour.
106    */
107  2 List<String> commands = new ArrayList<String>();
108  2 StringBuilder sb = new StringBuilder(256);
109  2 boolean firstColour = true;
110  2 for (Object key : colourMap.keySet())
111    {
112  8 Color colour = (Color) key;
113  8 String colourCode = ColorUtils.toTkCode(colour);
114  8 if (!firstColour)
115    {
116  6 sb.append("; ");
117    }
118  8 sb.append("color ").append(colourCode).append(" ");
119  8 firstColour = false;
120  8 final AtomSpecModel colourData = colourMap.get(colour);
121  8 sb.append(colourData.getAtomSpec());
122    }
123  2 commands.add(sb.toString());
124  2 return commands;
125    }
126   
127    /**
128    * Traverses a map of { modelNumber, {chain, {list of from-to ranges} } } and
129    * builds a Chimera format atom spec
130    *
131    * @param modelAndChainRanges
132    */
 
133  0 toggle protected static String getAtomSpec(
134    Map<Integer, Map<String, List<int[]>>> modelAndChainRanges)
135    {
136  0 StringBuilder sb = new StringBuilder(128);
137  0 boolean firstModelForColour = true;
138  0 for (Integer model : modelAndChainRanges.keySet())
139    {
140  0 boolean firstPositionForModel = true;
141  0 if (!firstModelForColour)
142    {
143  0 sb.append("|");
144    }
145  0 firstModelForColour = false;
146  0 sb.append("#").append(model).append(":");
147   
148  0 final Map<String, List<int[]>> modelData = modelAndChainRanges
149    .get(model);
150  0 for (String chain : modelData.keySet())
151    {
152  0 boolean hasChain = !"".equals(chain.trim());
153  0 for (int[] range : modelData.get(chain))
154    {
155  0 if (!firstPositionForModel)
156    {
157  0 sb.append(",");
158    }
159  0 if (range[0] == range[1])
160    {
161  0 sb.append(range[0]);
162    }
163    else
164    {
165  0 sb.append(range[0]).append("-").append(range[1]);
166    }
167  0 if (hasChain)
168    {
169  0 sb.append(".").append(chain);
170    }
171  0 firstPositionForModel = false;
172    }
173    }
174    }
175  0 return sb.toString();
176    }
177   
178    /**
179    * <pre>
180    * Build a data structure which records contiguous subsequences for each colour.
181    * From this we can easily generate the Chimera command for colour by sequence.
182    * Color
183    * Model number
184    * Chain
185    * list of start/end ranges
186    * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
187    * </pre>
188    */
 
189  1 toggle protected static Map<Object, AtomSpecModel> buildColoursMap(
190    StructureSelectionManager ssm, String[] files,
191    SequenceI[][] sequence, SequenceRenderer sr,
192    AlignmentViewPanel viewPanel)
193    {
194  1 FeatureRenderer fr = viewPanel.getFeatureRenderer();
195  1 FeatureColourFinder finder = new FeatureColourFinder(fr);
196  1 AlignViewportI viewport = viewPanel.getAlignViewport();
197  1 HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
198  1 AlignmentI al = viewport.getAlignment();
199  1 Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
200  1 Color lastColour = null;
201   
202  3 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
203    {
204  2 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
205   
206  2 if (mapping == null || mapping.length < 1)
207    {
208  0 continue;
209    }
210   
211  2 int startPos = -1, lastPos = -1;
212  2 String lastChain = "";
213  4 for (int s = 0; s < sequence[pdbfnum].length; s++)
214    {
215  4 for (int sp, m = 0; m < mapping.length; m++)
216    {
217  2 final SequenceI seq = sequence[pdbfnum][s];
218  ? if (mapping[m].getSequence() == seq
219    && (sp = al.findIndex(seq)) > -1)
220    {
221  2 SequenceI asp = al.getSequenceAt(sp);
222  22 for (int r = 0; r < asp.getLength(); r++)
223    {
224    // no mapping to gaps in sequence
225  20 if (Comparison.isGap(asp.getCharAt(r)))
226    {
227  0 continue;
228    }
229  20 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
230   
231  20 if (pos < 1 || pos == lastPos)
232    {
233  0 continue;
234    }
235   
236  20 Color colour = sr.getResidueColour(seq, r, finder);
237   
238    /*
239    * darker colour for hidden regions
240    */
241  20 if (!cs.isVisible(r))
242    {
243  6 colour = Color.GRAY;
244    }
245   
246  20 final String chain = mapping[m].getChain();
247   
248    /*
249    * Just keep incrementing the end position for this colour range
250    * _unless_ colour, PDB model or chain has changed, or there is a
251    * gap in the mapped residue sequence
252    */
253  20 final boolean newColour = !colour.equals(lastColour);
254  20 final boolean nonContig = lastPos + 1 != pos;
255  20 final boolean newChain = !chain.equals(lastChain);
256  20 if (newColour || nonContig || newChain)
257    {
258  8 if (startPos != -1)
259    {
260  6 addColourRange(colourMap, lastColour, pdbfnum, startPos,
261    lastPos, lastChain);
262    }
263  8 startPos = pos;
264    }
265  20 lastColour = colour;
266  20 lastPos = pos;
267  20 lastChain = chain;
268    }
269    // final colour range
270  2 if (lastColour != null)
271    {
272  2 addColourRange(colourMap, lastColour, pdbfnum, startPos,
273    lastPos, lastChain);
274    }
275    // break;
276    }
277    }
278    }
279    }
280  1 return colourMap;
281    }
282   
283    /**
284    * Helper method to add one contiguous colour range to the colour map.
285    *
286    * @param map
287    * @param key
288    * @param model
289    * @param startPos
290    * @param endPos
291    * @param chain
292    */
 
293  24 toggle protected static void addColourRange(Map<Object, AtomSpecModel> map,
294    Object key, int model, int startPos, int endPos, String chain)
295    {
296    /*
297    * Get/initialize map of data for the colour
298    */
299  24 AtomSpecModel atomSpec = map.get(key);
300  24 if (atomSpec == null)
301    {
302  11 atomSpec = new AtomSpecModel();
303  11 map.put(key, atomSpec);
304    }
305   
306  24 atomSpec.addRange(model, startPos, endPos, chain);
307    }
308   
309    /**
310    * Constructs and returns Chimera commands to set attributes on residues
311    * corresponding to features in Jalview. Attribute names are the Jalview
312    * feature type, with a "jv_" prefix.
313    *
314    * @param ssm
315    * @param files
316    * @param seqs
317    * @param viewPanel
318    * @return
319    */
 
320  0 toggle public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
321    StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
322    AlignmentViewPanel viewPanel)
323    {
324  0 Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
325    ssm, files, seqs, viewPanel);
326   
327  0 List<String> commands = buildSetAttributeCommands(featureMap);
328   
329  0 StructureMappingcommandSet cs = new StructureMappingcommandSet(
330    ChimeraCommands.class, null,
331    commands.toArray(new String[commands.size()]));
332   
333  0 return cs;
334    }
335   
336    /**
337    * <pre>
338    * Helper method to build a map of
339    * { featureType, { feature value, AtomSpecModel } }
340    * </pre>
341    *
342    * @param ssm
343    * @param files
344    * @param seqs
345    * @param viewPanel
346    * @return
347    */
 
348  0 toggle protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
349    StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
350    AlignmentViewPanel viewPanel)
351    {
352  0 Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
353   
354  0 FeatureRenderer fr = viewPanel.getFeatureRenderer();
355  0 if (fr == null)
356    {
357  0 return theMap;
358    }
359   
360  0 List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
361  0 if (visibleFeatures.isEmpty())
362    {
363  0 return theMap;
364    }
365   
366  0 AlignmentI alignment = viewPanel.getAlignment();
367  0 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
368    {
369  0 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
370   
371  0 if (mapping == null || mapping.length < 1)
372    {
373  0 continue;
374    }
375   
376  0 for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++)
377    {
378  0 for (int m = 0; m < mapping.length; m++)
379    {
380  0 final SequenceI seq = seqs[pdbfnum][seqNo];
381  0 int sp = alignment.findIndex(seq);
382  0 if (mapping[m].getSequence() == seq && sp > -1)
383    {
384    /*
385    * found a sequence with a mapping to a structure;
386    * now scan its features
387    */
388  0 SequenceI asp = alignment.getSequenceAt(sp);
389   
390  0 scanSequenceFeatures(visibleFeatures, mapping[m], asp, theMap,
391    pdbfnum);
392    }
393    }
394    }
395    }
396  0 return theMap;
397    }
398   
399    /**
400    * Inspect features on the sequence; for each feature that is visible,
401    * determine its mapped ranges in the structure (if any) according to the
402    * given mapping, and add them to the map
403    *
404    * @param visibleFeatures
405    * @param mapping
406    * @param seq
407    * @param theMap
408    * @param modelNumber
409    */
 
410  0 toggle protected static void scanSequenceFeatures(List<String> visibleFeatures,
411    StructureMapping mapping, SequenceI seq,
412    Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
413    {
414  0 List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures(
415    visibleFeatures.toArray(new String[visibleFeatures.size()]));
416  0 for (SequenceFeature sf : sfs)
417    {
418  0 String type = sf.getType();
419   
420    /*
421    * Only copy visible features, don't copy any which originated
422    * from Chimera, and suppress uninteresting ones (e.g. RESNUM)
423    */
424  0 boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
425    .equals(sf.getFeatureGroup());
426  0 if (isFromViewer)
427    {
428  0 continue;
429    }
430  0 List<int[]> mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(),
431    sf.getEnd());
432   
433  0 if (!mappedRanges.isEmpty())
434    {
435  0 String value = sf.getDescription();
436  0 if (value == null || value.length() == 0)
437    {
438  0 value = type;
439    }
440  0 float score = sf.getScore();
441  0 if (score != 0f && !Float.isNaN(score))
442    {
443  0 value = Float.toString(score);
444    }
445  0 Map<Object, AtomSpecModel> featureValues = theMap.get(type);
446  0 if (featureValues == null)
447    {
448  0 featureValues = new HashMap<Object, AtomSpecModel>();
449  0 theMap.put(type, featureValues);
450    }
451  0 for (int[] range : mappedRanges)
452    {
453  0 addColourRange(featureValues, value, modelNumber, range[0],
454    range[1], mapping.getChain());
455    }
456    }
457    }
458    }
459   
460    /**
461    * Traverse the map of features/values/models/chains/positions to construct a
462    * list of 'setattr' commands (one per distinct feature type and value).
463    * <p>
464    * The format of each command is
465    *
466    * <pre>
467    * <blockquote> setattr r <featureName> " " #modelnumber:range.chain
468    * e.g. setattr r jv:chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
469    * </blockquote>
470    * </pre>
471    *
472    * @param featureMap
473    * @return
474    */
 
475  5 toggle protected static List<String> buildSetAttributeCommands(
476    Map<String, Map<Object, AtomSpecModel>> featureMap)
477    {
478  5 List<String> commands = new ArrayList<String>();
479  5 for (String featureType : featureMap.keySet())
480    {
481  5 String attributeName = makeAttributeName(featureType);
482   
483    /*
484    * clear down existing attributes for this feature
485    */
486    // 'problem' - sets attribute to None on all residues - overkill?
487    // commands.add("~setattr r " + attributeName + " :*");
488   
489  5 Map<Object, AtomSpecModel> values = featureMap.get(featureType);
490  5 for (Object value : values.keySet())
491    {
492    /*
493    * for each distinct value recorded for this feature type,
494    * add a command to set the attribute on the mapped residues
495    * Put values in single quotes, encoding any embedded single quotes
496    */
497  6 StringBuilder sb = new StringBuilder(128);
498  6 String featureValue = value.toString();
499  6 featureValue = featureValue.replaceAll("\\'", "&#39;");
500  6 sb.append("setattr r ").append(attributeName).append(" '")
501    .append(featureValue).append("' ");
502  6 sb.append(values.get(value).getAtomSpec());
503  6 commands.add(sb.toString());
504    }
505    }
506   
507  5 return commands;
508    }
509   
510    /**
511    * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied
512    * for a 'Jalview' namespace, and any non-alphanumeric character is converted
513    * to an underscore.
514    *
515    * @param featureType
516    * @return
517    *
518    * <pre>
519    * &#64;see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
520    * </pre>
521    */
 
522  11 toggle protected static String makeAttributeName(String featureType)
523    {
524  11 StringBuilder sb = new StringBuilder();
525  11 if (featureType != null)
526    {
527  10 for (char c : featureType.toCharArray())
528    {
529  93 sb.append(Character.isLetterOrDigit(c) ? c : '_');
530    }
531    }
532  11 String attName = NAMESPACE_PREFIX + sb.toString();
533   
534    /*
535    * Chimera treats an attribute name ending in 'color' as colour-valued;
536    * Jalview doesn't, so prevent this by appending an underscore
537    */
538  11 if (attName.toUpperCase().endsWith("COLOR"))
539    {
540  1 attName += "_";
541    }
542   
543  11 return attName;
544    }
545   
546    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.