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Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.ext.jmol

File JmolCommands.java

 

Coverage histogram

../../../img/srcFileCovDistChart8.png
20% of files have more coverage

Code metrics

46
118
20
1
484
314
49
0.42
5.9
20
2.45

Classes

Class Line # Actions
JmolCommands 52 118 49
0.733695673.4%
 

Contributing tests

This file is covered by 17 tests. .

Source view

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.jmol;
22   
23    import java.awt.Color;
24    import java.util.ArrayList;
25    import java.util.Arrays;
26    import java.util.List;
27    import java.util.Map;
28   
29    import jalview.api.AlignViewportI;
30    import jalview.api.AlignmentViewPanel;
31    import jalview.api.FeatureRenderer;
32    import jalview.api.SequenceRenderer;
33    import jalview.datamodel.AlignmentI;
34    import jalview.datamodel.HiddenColumns;
35    import jalview.datamodel.SequenceI;
36    import jalview.renderer.seqfeatures.FeatureColourFinder;
37    import jalview.structure.AtomSpecModel;
38    import jalview.structure.StructureCommand;
39    import jalview.structure.StructureCommandI;
40    import jalview.structure.StructureCommandsBase;
41    import jalview.structure.StructureMapping;
42    import jalview.structure.StructureSelectionManager;
43    import jalview.util.Comparison;
44    import jalview.util.Platform;
45   
46    /**
47    * Routines for generating Jmol commands for Jalview/Jmol binding
48    *
49    * @author JimP
50    *
51    */
 
52    public class JmolCommands extends StructureCommandsBase
53    {
54    private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
55    "select *; cartoons off; backbone");
56   
57    private static final StructureCommand FOCUS_VIEW = new StructureCommand("zoom 0");
58   
59    private static final StructureCommand COLOUR_ALL_WHITE = new StructureCommand(
60    "select *;color white;");
61   
62    private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
63    "select *;color white;select ASP,GLU;color red;"
64    + "select LYS,ARG;color blue;select CYS;color yellow");
65   
66    private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
67    "select *;color chain");
68   
69    private static final String PIPE = "|";
70   
71    private static final String HYPHEN = "-";
72   
73    private static final String COLON = ":";
74   
75    private static final String SLASH = "/";
76   
77    /**
78    * {@inheritDoc}
79    *
80    * @return
81    */
 
82  1 toggle @Override
83    public int getModelStartNo()
84    {
85  1 return 1;
86    }
87   
88    /**
89    * Returns a string representation of the given colour suitable for inclusion
90    * in Jmol commands
91    *
92    * @param c
93    * @return
94    */
 
95  32 toggle protected String getColourString(Color c)
96    {
97  32 return c == null ? null
98    : String.format("[%d,%d,%d]", c.getRed(), c.getGreen(),
99    c.getBlue());
100    }
101   
 
102  1 toggle @Override
103    public StructureCommandI colourByChain()
104    {
105  1 return COLOUR_BY_CHAIN;
106    }
107   
 
108  1 toggle @Override
109    public List<StructureCommandI> colourByCharge()
110    {
111  1 return Arrays.asList(COLOUR_BY_CHARGE);
112    }
113   
 
114  0 toggle @Override
115    public List<StructureCommandI> colourByResidues(Map<String, Color> colours)
116    {
117  0 List<StructureCommandI> cmds = super.colourByResidues(colours);
118  0 cmds.add(0, COLOUR_ALL_WHITE);
119  0 return cmds;
120    }
121   
 
122  1 toggle @Override
123    public StructureCommandI setBackgroundColour(Color col)
124    {
125  1 return new StructureCommand("background " + getColourString(col));
126    }
127   
 
128  1 toggle @Override
129    public StructureCommandI focusView()
130    {
131  1 return FOCUS_VIEW;
132    }
133   
 
134  0 toggle @Override
135    public List<StructureCommandI> showChains(List<String> toShow)
136    {
137  0 StringBuilder atomSpec = new StringBuilder(128);
138  0 boolean first = true;
139  0 for (String chain : toShow)
140    {
141  0 String[] tokens = chain.split(":");
142  0 if (tokens.length == 2)
143    {
144  0 if (!first)
145    {
146  0 atomSpec.append(" or ");
147    }
148  0 first = false;
149  0 atomSpec.append(":").append(tokens[1]).append(" /").append(tokens[0]);
150    }
151    }
152   
153  0 String spec = atomSpec.toString();
154  0 String command = "select *;restrict " + spec + ";cartoon;center "
155    + spec;
156  0 return Arrays.asList(new StructureCommand(command));
157    }
158   
159    /**
160    * Returns a command to superpose atoms in {@code atomSpec} to those in
161    * {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna).
162    * For example
163    *
164    * <pre>
165    * compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1}
166    * ATOMS {1-87:A}{2-54:A|61-94:A} ROTATE TRANSLATE 1.0;
167    * </pre>
168    *
169    * where {@code conformation=1} excludes ALTLOC atom locations, and 1.0 is the
170    * time in seconds to animate the action. For this example, atoms in model 2
171    * are moved towards atoms in model 1.
172    * <p>
173    * The two atomspecs should each be for one model only, but may have more than
174    * one chain. The number of atoms specified should be the same for both
175    * models, though if not, Jmol may make a 'best effort' at superposition.
176    *
177    * @see https://chemapps.stolaf.edu/jmol/docs/#compare
178    */
 
179  1 toggle @Override
180    public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
181    AtomSpecModel atomSpec)
182    {
183  1 StringBuilder sb = new StringBuilder(64);
184  1 String refModel = refAtoms.getModels().iterator().next();
185  1 String model2 = atomSpec.getModels().iterator().next();
186  1 sb.append(String.format("compare {%s.1} {%s.1}", model2, refModel));
187  1 sb.append(" SUBSET {(*.CA | *.P) and conformation=1} ATOMS {");
188   
189    /*
190    * command examples don't include modelspec with atoms, getAtomSpec does;
191    * it works, so leave it as it is for simplicity
192    */
193  1 sb.append(getAtomSpec(atomSpec, true)).append("}{");
194  1 sb.append(getAtomSpec(refAtoms, true)).append("}");
195  1 sb.append(" ROTATE TRANSLATE ");
196  1 sb.append(getCommandSeparator());
197   
198    /*
199    * show residues used for superposition as ribbon
200    */
201  1 sb.append("select ").append(getAtomSpec(atomSpec, false)).append("|");
202  1 sb.append(getAtomSpec(refAtoms, false)).append(getCommandSeparator())
203    .append("cartoons");
204   
205  1 return Arrays.asList(new StructureCommand(sb.toString()));
206    }
207   
 
208  0 toggle @Override
209    public StructureCommandI openCommandFile(String path)
210    {
211    /*
212    * https://chemapps.stolaf.edu/jmol/docs/#script
213    * not currently used in Jalview
214    */
215  0 return new StructureCommand("script " + path);
216    }
217   
 
218  3 toggle @Override
219    public StructureCommandI saveSession(String filepath)
220    {
221    /*
222    * https://chemapps.stolaf.edu/jmol/docs/#writemodel
223    */
224  3 return new StructureCommand("write STATE \"" + filepath + "\"");
225    }
226   
 
227  11 toggle @Override
228    protected StructureCommandI colourResidues(String atomSpec, Color colour)
229    {
230  11 StringBuilder sb = new StringBuilder(atomSpec.length()+20);
231  11 sb.append("select ").append(atomSpec).append(getCommandSeparator())
232    .append("color").append(getColourString(colour));
233  11 return new StructureCommand(sb.toString());
234    }
235   
 
236  0 toggle @Override
237    protected String getResidueSpec(String residue)
238    {
239  0 return residue;
240    }
241   
242    /**
243    * Generates a Jmol atomspec string like
244    *
245    * <pre>
246    * 2-5:A/1.1,8:A/1.1,5-10:B/2.1
247    * </pre>
248    *
249    * Parameter {@code alphaOnly} is not used here - this restriction is made by
250    * a separate clause in the {@code compare} (superposition) command.
251    */
 
252  26 toggle @Override
253    public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
254    {
255  26 StringBuilder sb = new StringBuilder(128);
256   
257  26 boolean first = true;
258  26 for (String modelNo : model.getModels())
259    {
260  35 for (String chain : model.getChains(modelNo))
261    {
262  54 for (int[] range : model.getRanges(modelNo, chain))
263    {
264  69 if (!first)
265    {
266  44 sb.append(PIPE);
267    }
268  69 first = false;
269  69 if (range[0] == range[1])
270    {
271  16 sb.append(range[0]);
272    }
273    else
274    {
275  53 sb.append(range[0]).append(HYPHEN).append(range[1]);
276    }
277  69 sb.append(COLON).append(chain.trim()).append(SLASH);
278  69 sb.append(String.valueOf(modelNo)).append(".1");
279    }
280    }
281    }
282   
283  26 return sb.toString();
284    }
285   
 
286  2 toggle @Override
287    public List<StructureCommandI> showBackbone()
288    {
289  2 return Arrays.asList(SHOW_BACKBONE);
290    }
291   
 
292  4 toggle @Override
293    public StructureCommandI loadFile(String file)
294    {
295    // https://chemapps.stolaf.edu/jmol/docs/#loadfiles
296  4 return new StructureCommand("load FILES \"" +
297    Platform.escapeBackslashes(file) + "\"");
298    }
299   
300    /**
301    * Obsolete method, only referenced from
302    * jalview.javascript.MouseOverStructureListener
303    *
304    * @param ssm
305    * @param files
306    * @param sequence
307    * @param sr
308    * @param viewPanel
309    * @return
310    */
 
311  1 toggle @Deprecated
312    public String[] colourBySequence(StructureSelectionManager ssm,
313    String[] files, SequenceI[][] sequence, SequenceRenderer sr,
314    AlignmentViewPanel viewPanel)
315    {
316    // TODO delete method
317   
318  1 FeatureRenderer fr = viewPanel.getFeatureRenderer();
319  1 FeatureColourFinder finder = new FeatureColourFinder(fr);
320  1 AlignViewportI viewport = viewPanel.getAlignViewport();
321  1 HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
322  1 AlignmentI al = viewport.getAlignment();
323  1 List<String> cset = new ArrayList<>();
324   
325  3 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
326    {
327  2 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
328  2 StringBuilder command = new StringBuilder(128);
329  2 List<String> str = new ArrayList<>();
330   
331  2 if (mapping == null || mapping.length < 1)
332    {
333  0 continue;
334    }
335   
336  4 for (int s = 0; s < sequence[pdbfnum].length; s++)
337    {
338  4 for (int sp, m = 0; m < mapping.length; m++)
339    {
340  ? if (mapping[m].getSequence() == sequence[pdbfnum][s]
341    && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
342    {
343  2 int lastPos = StructureMapping.UNASSIGNED_VALUE;
344  2 SequenceI asp = al.getSequenceAt(sp);
345  22 for (int r = 0; r < asp.getLength(); r++)
346    {
347    // no mapping to gaps in sequence
348  20 if (Comparison.isGap(asp.getCharAt(r)))
349    {
350  0 continue;
351    }
352  20 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
353   
354  20 if (pos == lastPos)
355    {
356  0 continue;
357    }
358  20 if (pos == StructureMapping.UNASSIGNED_VALUE)
359    {
360    // terminate current colour op
361  0 if (command.length() > 0
362    && command.charAt(command.length() - 1) != ';')
363    {
364  0 command.append(";");
365    }
366    // reset lastPos
367  0 lastPos = StructureMapping.UNASSIGNED_VALUE;
368  0 continue;
369    }
370   
371  20 lastPos = pos;
372   
373  20 Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
374    finder);
375   
376    /*
377    * shade hidden regions darker
378    */
379  20 if (!cs.isVisible(r))
380    {
381  6 col = Color.GRAY;
382    }
383   
384  20 String newSelcom = (mapping[m].getChain() != " "
385    ? ":" + mapping[m].getChain()
386    : "") + "/" + (pdbfnum + 1) + ".1" + ";color"
387    + getColourString(col);
388  20 if (command.length() > newSelcom.length() && command
389    .substring(command.length() - newSelcom.length())
390    .equals(newSelcom))
391    {
392  12 command = JmolCommands.condenseCommand(command, pos);
393  12 continue;
394    }
395    // TODO: deal with case when buffer is too large for Jmol to parse
396    // - execute command and flush
397   
398  8 if (command.length() > 0
399    && command.charAt(command.length() - 1) != ';')
400    {
401  6 command.append(";");
402    }
403   
404  8 if (command.length() > 51200)
405    {
406    // add another chunk
407  0 str.add(command.toString());
408  0 command.setLength(0);
409    }
410  8 command.append("select " + pos);
411  8 command.append(newSelcom);
412    }
413    // break;
414    }
415    }
416    }
417    {
418    // add final chunk
419  2 str.add(command.toString());
420  2 command.setLength(0);
421    }
422  2 cset.addAll(str);
423   
424    }
425  1 return cset.toArray(new String[cset.size()]);
426    }
427   
428    /**
429    * Helper method
430    *
431    * @param command
432    * @param pos
433    * @return
434    */
 
435  12 toggle @Deprecated
436    private static StringBuilder condenseCommand(
437    StringBuilder command,
438    int pos)
439    {
440   
441    // work back to last 'select'
442  12 int p = command.length(), q = p;
443  12 do
444    {
445  74 p -= 6;
446  74 if (p < 1)
447    {
448  0 p = 0;
449    }
450  74 ;
451  ? } while ((q = command.indexOf("select", p)) == -1 && p > 0);
452   
453  12 StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
454   
455  12 command = command.delete(0, q + 7);
456   
457  12 String start;
458   
459  12 if (command.indexOf("-") > -1)
460    {
461  8 start = command.substring(0, command.indexOf("-"));
462    }
463    else
464    {
465  4 start = command.substring(0, command.indexOf(":"));
466    }
467   
468  12 sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
469   
470  12 return sb;
471    }
472   
 
473  2 toggle @Override
474    public StructureCommandI openSession(String filepath)
475    {
476  2 return loadFile(filepath);
477    }
478   
 
479  1 toggle @Override
480    public StructureCommandI closeViewer()
481    {
482  1 return null; // not an external viewer
483    }
484    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.