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JmolParser | 67 | 253 | 116 |
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.io.File; | |
24 | import java.io.IOException; | |
25 | import java.util.ArrayList; | |
26 | import java.util.HashMap; | |
27 | import java.util.List; | |
28 | import java.util.Locale; | |
29 | import java.util.Map; | |
30 | import java.util.Vector; | |
31 | ||
32 | import org.jmol.api.JmolStatusListener; | |
33 | import org.jmol.api.JmolViewer; | |
34 | import org.jmol.c.CBK; | |
35 | import org.jmol.c.STR; | |
36 | import org.jmol.modelset.ModelSet; | |
37 | import org.jmol.viewer.Viewer; | |
38 | ||
39 | import com.stevesoft.pat.Regex; | |
40 | ||
41 | import jalview.bin.Console; | |
42 | import jalview.datamodel.Alignment; | |
43 | import jalview.datamodel.AlignmentAnnotation; | |
44 | import jalview.datamodel.Annotation; | |
45 | import jalview.datamodel.PDBEntry; | |
46 | import jalview.datamodel.SequenceI; | |
47 | import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder; | |
48 | import jalview.datamodel.annotations.AnnotationRowBuilder; | |
49 | import jalview.io.DataSourceType; | |
50 | import jalview.io.FileParse; | |
51 | import jalview.io.StructureFile; | |
52 | import jalview.schemes.ResidueProperties; | |
53 | import jalview.structure.StructureImportSettings; | |
54 | import jalview.util.Format; | |
55 | import jalview.util.MessageManager; | |
56 | import jalview.ws.dbsources.EBIAlfaFold; | |
57 | import mc_view.Atom; | |
58 | import mc_view.PDBChain; | |
59 | import mc_view.Residue; | |
60 | ||
61 | /** | |
62 | * Import and process files with Jmol for file like PDB, mmCIF | |
63 | * | |
64 | * @author jprocter | |
65 | * | |
66 | */ | |
67 | public class JmolParser extends StructureFile implements JmolStatusListener | |
68 | { | |
69 | Viewer viewer = null; | |
70 | ||
71 | 149 | public JmolParser(boolean immediate, Object inFile, |
72 | DataSourceType sourceType) throws IOException | |
73 | { | |
74 | // BH 2018 File or String for filename | |
75 | 149 | super(immediate, inFile, sourceType); |
76 | ||
77 | } | |
78 | ||
79 | 6 | public JmolParser(Object inFile, DataSourceType sourceType) |
80 | throws IOException | |
81 | { | |
82 | 6 | this(inFile, sourceType, null); |
83 | } | |
84 | ||
85 | 21 | public JmolParser(Object inFile, DataSourceType sourceType, |
86 | StructureImportSettings.TFType tempfacType) throws IOException | |
87 | { | |
88 | 21 | super(inFile, sourceType, tempfacType); |
89 | } | |
90 | ||
91 | 5 | public JmolParser(FileParse fp, boolean doXferSettings) throws IOException |
92 | { | |
93 | 5 | super(fp, doXferSettings); |
94 | } | |
95 | ||
96 | 0 | public JmolParser(FileParse fp) throws IOException |
97 | { | |
98 | 0 | super(fp); |
99 | } | |
100 | ||
101 | 1 | public JmolParser() |
102 | { | |
103 | } | |
104 | ||
105 | /** | |
106 | * Calls the Jmol library to parse the PDB/mmCIF file, and then inspects the | |
107 | * resulting object model to generate Jalview-style sequences, with secondary | |
108 | * structure annotation added where available (i.e. where it has been computed | |
109 | * by Jmol using DSSP). | |
110 | * | |
111 | * @see jalview.io.AlignFile#parse() | |
112 | */ | |
113 | 0 | @Override |
114 | public void parse() throws IOException | |
115 | { | |
116 | 0 | parse(true); |
117 | } | |
118 | ||
119 | 175 | @Override |
120 | public void parse(boolean doXferSettings) throws IOException | |
121 | { | |
122 | 175 | setChains(new Vector<PDBChain>()); |
123 | 175 | Viewer jmolModel = getJmolData(); |
124 | 175 | jmolModel.openReader(getDataName(), getDataName(), getReader()); |
125 | 175 | waitForScript(jmolModel); |
126 | ||
127 | /* | |
128 | * Convert one or more Jmol Model objects to Jalview sequences | |
129 | */ | |
130 | 175 | if (jmolModel.ms.mc > 0) |
131 | { | |
132 | // ideally we do this | |
133 | // try | |
134 | // { | |
135 | // setStructureFileType(jmolModel.evalString("show _fileType")); | |
136 | // } catch (Exception q) | |
137 | // { | |
138 | // } | |
139 | // ; | |
140 | // instead, we distinguish .cif from non-.cif by filename | |
141 | 175 | setStructureFileType( |
142 | 175 | getDataName().toLowerCase(Locale.ROOT).endsWith(".cif") |
143 | ? PDBEntry.Type.MMCIF.toString() | |
144 | : "PDB"); | |
145 | ||
146 | 175 | transformJmolModelToJalview(jmolModel.ms, doXferSettings); |
147 | } | |
148 | } | |
149 | ||
150 | /** | |
151 | * create a headless jmol instance for dataprocessing | |
152 | * | |
153 | * @return | |
154 | */ | |
155 | 175 | private Viewer getJmolData() |
156 | { | |
157 | 175 | if (viewer == null) |
158 | { | |
159 | 175 | try |
160 | { | |
161 | /* | |
162 | * params -o (output to sysout) -n (nodisplay) -x (exit when finished) | |
163 | * see http://wiki.jmol.org/index.php/Jmol_Application | |
164 | */ | |
165 | ||
166 | 175 | viewer = JalviewJmolBinding.getJmolData(this); |
167 | // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used | |
168 | 175 | viewer.setBooleanProperty("defaultStructureDSSP", true); |
169 | } catch (ClassCastException x) | |
170 | { | |
171 | 0 | throw new Error(MessageManager.formatMessage( |
172 | "error.jmol_version_not_compatible_with_jalview_version", | |
173 | new String[] | |
174 | { JmolViewer.getJmolVersion() }), x); | |
175 | } | |
176 | } | |
177 | 175 | return viewer; |
178 | } | |
179 | ||
180 | 175 | public static Regex getNewAlphafoldValidator() |
181 | { | |
182 | 175 | Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)"); |
183 | 175 | validator.setIgnoreCase(true); |
184 | 175 | return validator; |
185 | } | |
186 | ||
187 | PDBEntry.Type jmolFiletype = null; | |
188 | ||
189 | /** | |
190 | * resolve a jmol filetype string and update the jmolFiletype field | |
191 | * accordingly | |
192 | * | |
193 | * @param jmolIdentifiedFileType | |
194 | * @return true if filetype was identified as MMCIF, PDB | |
195 | */ | |
196 | 175 | public boolean updateFileType(String jmolIdentifiedFileType) |
197 | { | |
198 | 175 | if (jmolIdentifiedFileType == null |
199 | || jmolIdentifiedFileType.trim().equals("")) | |
200 | { | |
201 | 0 | return false; |
202 | } | |
203 | 175 | if ("mmcif".equalsIgnoreCase(jmolIdentifiedFileType)) |
204 | { | |
205 | 18 | jmolFiletype = PDBEntry.Type.MMCIF; |
206 | 18 | return true; |
207 | } | |
208 | 157 | if ("pdb".equalsIgnoreCase(jmolIdentifiedFileType)) |
209 | { | |
210 | 157 | jmolFiletype = PDBEntry.Type.PDB; |
211 | 157 | return true; |
212 | } | |
213 | 0 | return false; |
214 | } | |
215 | ||
216 | 175 | public void transformJmolModelToJalview(ModelSet ms, |
217 | boolean localDoXferSettings) throws IOException | |
218 | { | |
219 | 175 | try |
220 | { | |
221 | 175 | Regex alphaFold = getNewAlphafoldValidator(); |
222 | 175 | String lastID = ""; |
223 | 175 | List<SequenceI> rna = new ArrayList<SequenceI>(); |
224 | 175 | List<SequenceI> prot = new ArrayList<SequenceI>(); |
225 | 175 | PDBChain tmpchain; |
226 | 175 | String pdbId = (String) ms.getInfo(0, "title"); |
227 | 175 | boolean isMMCIF = false; |
228 | 175 | String jmolFileType_String = (String) ms.getInfo(0, "fileType"); |
229 | 175 | if (updateFileType(jmolFileType_String)) |
230 | { | |
231 | 175 | setStructureFileType(jmolFiletype.toString()); |
232 | } | |
233 | ||
234 | 175 | isMMCIF = PDBEntry.Type.MMCIF.equals(jmolFiletype); |
235 | ||
236 | 175 | if (pdbId == null) |
237 | { | |
238 | 60 | setId(safeName(getDataName())); |
239 | 60 | setPDBIdAvailable(false); |
240 | } | |
241 | else | |
242 | { | |
243 | 115 | setId(pdbId); |
244 | 115 | setPDBIdAvailable(true); |
245 | 115 | setAlphafoldModel(alphaFold.search(pdbId) && isMMCIF); |
246 | } | |
247 | 175 | List<Atom> significantAtoms = convertSignificantAtoms(ms); |
248 | 175 | for (Atom tmpatom : significantAtoms) |
249 | { | |
250 | 40945 | if (tmpatom.resNumIns.trim().equals(lastID)) |
251 | { | |
252 | // phosphorylated protein - seen both CA and P.. | |
253 | 1 | continue; |
254 | } | |
255 | 40944 | tmpchain = findChain(tmpatom.chain); |
256 | 40944 | if (tmpchain != null) |
257 | { | |
258 | 40677 | tmpchain.atoms.addElement(tmpatom); |
259 | } | |
260 | else | |
261 | { | |
262 | 267 | AnnotationRowBuilder builder = null; |
263 | 267 | if (isAlphafoldModel() |
264 | || getTemperatureFactorType() == StructureImportSettings.TFType.PLDDT) | |
265 | { | |
266 | 34 | builder = new AlphaFoldAnnotationRowBuilder(); |
267 | } | |
268 | ||
269 | 267 | tmpchain = new PDBChain(getId(), tmpatom.chain, builder); |
270 | 267 | getChains().add(tmpchain); |
271 | 267 | tmpchain.atoms.addElement(tmpatom); |
272 | } | |
273 | 40944 | lastID = tmpatom.resNumIns.trim(); |
274 | } | |
275 | 175 | if (isParseImmediately() && localDoXferSettings) |
276 | { | |
277 | // configure parsing settings from the static singleton | |
278 | 118 | xferSettings(); |
279 | } | |
280 | ||
281 | 175 | makeResidueList(); |
282 | 175 | makeCaBondList(); |
283 | ||
284 | 175 | for (PDBChain chain : getChains()) |
285 | { | |
286 | 267 | SequenceI chainseq = postProcessChain(chain); |
287 | 267 | if (isRNA(chainseq)) |
288 | { | |
289 | 0 | rna.add(chainseq); |
290 | } | |
291 | else | |
292 | { | |
293 | 267 | prot.add(chainseq); |
294 | } | |
295 | ||
296 | // look at local setting for adding secondary tructure | |
297 | 267 | if (predictSecondaryStructure) |
298 | { | |
299 | 237 | createAnnotation(chainseq, chain, ms.at); |
300 | } | |
301 | } | |
302 | // if Alphafold, fetch the PAE matrix if doesn't already have one | |
303 | 175 | if (isAlphafoldModel() && !hasPAEMatrix()) |
304 | { | |
305 | 6 | try |
306 | { | |
307 | 6 | Console.info("Retrieving PAE for " + pdbId); |
308 | 6 | File paeFile = EBIAlfaFold.fetchAlphaFoldPAE(pdbId, null); |
309 | 6 | this.setPAEMatrix(paeFile.getAbsolutePath()); |
310 | } catch (Throwable t) | |
311 | { | |
312 | 0 | Console.error("Couldn't get the pAE for " + pdbId, t); |
313 | } | |
314 | } | |
315 | // add a PAEMatrix if set (either by above or otherwise) | |
316 | 175 | if (hasPAEMatrix()) |
317 | { | |
318 | 42 | try |
319 | { | |
320 | 42 | Alignment al = new Alignment(prot.toArray(new SequenceI[0])); |
321 | 42 | EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0, |
322 | null, false, false, null); | |
323 | ||
324 | 42 | if (al.getAlignmentAnnotation() != null) |
325 | { | |
326 | 42 | for (AlignmentAnnotation alann : al.getAlignmentAnnotation()) |
327 | { | |
328 | 42 | annotations.add(alann); |
329 | } | |
330 | } | |
331 | } catch (Throwable ff) | |
332 | { | |
333 | 0 | Console.error("Couldn't import PAE Matrix from " + getPAEMatrix(), |
334 | ff); | |
335 | 0 | warningMessage += "Couldn't import PAE Matrix" |
336 | + getNewlineString() + ff.getLocalizedMessage() | |
337 | + getNewlineString(); | |
338 | } | |
339 | } | |
340 | } catch (OutOfMemoryError er) | |
341 | { | |
342 | 0 | jalview.bin.Console.outPrintln( |
343 | "OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL"); | |
344 | 0 | throw new IOException(MessageManager |
345 | .getString("exception.outofmemory_loading_mmcif_file")); | |
346 | } | |
347 | } | |
348 | ||
349 | 175 | private List<Atom> convertSignificantAtoms(ModelSet ms) |
350 | { | |
351 | 175 | List<Atom> significantAtoms = new ArrayList<Atom>(); |
352 | 175 | HashMap<String, org.jmol.modelset.Atom> chainTerMap = new HashMap<String, org.jmol.modelset.Atom>(); |
353 | 175 | org.jmol.modelset.Atom prevAtom = null; |
354 | 175 | for (org.jmol.modelset.Atom atom : ms.at) |
355 | { | |
356 | 210765 | if (atom.getAtomName().equalsIgnoreCase("CA") |
357 | || atom.getAtomName().equalsIgnoreCase("P")) | |
358 | { | |
359 | 40973 | if (!atomValidated(atom, prevAtom, chainTerMap)) |
360 | { | |
361 | 24 | continue; |
362 | } | |
363 | 40949 | Atom curAtom = new Atom(atom.x, atom.y, atom.z); |
364 | 40949 | curAtom.atomIndex = atom.getIndex(); |
365 | 40949 | curAtom.chain = atom.getChainIDStr(); |
366 | 40949 | curAtom.insCode = atom.group.getInsertionCode() == '\000' ? ' ' |
367 | : atom.group.getInsertionCode(); | |
368 | 40949 | curAtom.name = atom.getAtomName(); |
369 | 40949 | curAtom.number = atom.getAtomNumber(); |
370 | 40949 | curAtom.resName = atom.getGroup3(true); |
371 | 40949 | curAtom.resNumber = atom.getResno(); |
372 | 40949 | curAtom.occupancy = ms.occupancies != null |
373 | ? ms.occupancies[atom.getIndex()] | |
374 | : Float.valueOf(atom.getOccupancy100()); | |
375 | 40949 | String fmt = new Format("%4i").form(curAtom.resNumber); |
376 | 40949 | curAtom.resNumIns = (fmt + curAtom.insCode); |
377 | 40949 | curAtom.tfactor = atom.getBfactor100() / 100f; |
378 | 40949 | curAtom.type = 0; |
379 | // significantAtoms.add(curAtom); | |
380 | // ignore atoms from subsequent models | |
381 | 40949 | if (!significantAtoms.contains(curAtom)) |
382 | { | |
383 | 40945 | significantAtoms.add(curAtom); |
384 | } | |
385 | 40949 | prevAtom = atom; |
386 | } | |
387 | } | |
388 | 175 | return significantAtoms; |
389 | } | |
390 | ||
391 | 40973 | private boolean atomValidated(org.jmol.modelset.Atom curAtom, |
392 | org.jmol.modelset.Atom prevAtom, | |
393 | HashMap<String, org.jmol.modelset.Atom> chainTerMap) | |
394 | { | |
395 | // jalview.bin.Console.outPrintln("Atom: " + curAtom.getAtomNumber() | |
396 | // + " Last atom index " + curAtom.group.lastAtomIndex); | |
397 | 40973 | if (chainTerMap == null || prevAtom == null) |
398 | { | |
399 | 175 | return true; |
400 | } | |
401 | 40798 | String curAtomChId = curAtom.getChainIDStr(); |
402 | 40798 | String prevAtomChId = prevAtom.getChainIDStr(); |
403 | // new chain encoutered | |
404 | 40798 | if (!prevAtomChId.equals(curAtomChId)) |
405 | { | |
406 | // On chain switch add previous chain termination to xTerMap if not exists | |
407 | 116 | if (!chainTerMap.containsKey(prevAtomChId)) |
408 | { | |
409 | 104 | chainTerMap.put(prevAtomChId, prevAtom); |
410 | } | |
411 | // if current atom belongs to an already terminated chain and the resNum | |
412 | // diff < 5 then mark as valid and update termination Atom | |
413 | 116 | if (chainTerMap.containsKey(curAtomChId)) |
414 | { | |
415 | 24 | if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno()) |
416 | { | |
417 | 0 | return false; |
418 | } | |
419 | 24 | if ((curAtom.getResno() |
420 | - chainTerMap.get(curAtomChId).getResno()) < 5) | |
421 | { | |
422 | 0 | chainTerMap.put(curAtomChId, curAtom); |
423 | 0 | return true; |
424 | } | |
425 | 24 | return false; |
426 | } | |
427 | } | |
428 | // atom with previously terminated chain encountered | |
429 | 40682 | else if (chainTerMap.containsKey(curAtomChId)) |
430 | { | |
431 | 0 | if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno()) |
432 | { | |
433 | 0 | return false; |
434 | } | |
435 | 0 | if ((curAtom.getResno() |
436 | - chainTerMap.get(curAtomChId).getResno()) < 5) | |
437 | { | |
438 | 0 | chainTerMap.put(curAtomChId, curAtom); |
439 | 0 | return true; |
440 | } | |
441 | 0 | return false; |
442 | } | |
443 | // HETATM with resNum jump > 2 | |
444 | 40774 | return !(curAtom.isHetero() |
445 | && ((curAtom.getResno() - prevAtom.getResno()) > 2)); | |
446 | } | |
447 | ||
448 | 237 | private void createAnnotation(SequenceI sequence, PDBChain chain, |
449 | org.jmol.modelset.Atom[] jmolAtoms) | |
450 | { | |
451 | 237 | char[] secstr = new char[sequence.getLength()]; |
452 | 237 | char[] secstrcode = new char[sequence.getLength()]; |
453 | ||
454 | // Ensure Residue size equals Seq size | |
455 | 237 | if (chain.residues.size() != sequence.getLength()) |
456 | { | |
457 | 0 | return; |
458 | } | |
459 | 237 | int annotIndex = 0; |
460 | 237 | for (Residue residue : chain.residues) |
461 | { | |
462 | 37678 | Atom repAtom = residue.getAtoms().get(0); |
463 | 37678 | STR proteinStructureSubType = jmolAtoms[repAtom.atomIndex].group |
464 | .getProteinStructureSubType(); | |
465 | 37678 | setSecondaryStructure(proteinStructureSubType, annotIndex, secstr, |
466 | secstrcode); | |
467 | 37678 | ++annotIndex; |
468 | } | |
469 | 237 | addSecondaryStructureAnnotation(chain.pdbid, sequence, secstr, |
470 | secstrcode, chain.id, sequence.getStart()); | |
471 | } | |
472 | ||
473 | /** | |
474 | * Helper method that adds an AlignmentAnnotation for secondary structure to | |
475 | * the sequence, provided at least one secondary structure assignment has been | |
476 | * made | |
477 | * | |
478 | * @param modelTitle | |
479 | * @param seq | |
480 | * @param secstr | |
481 | * @param secstrcode | |
482 | * @param chainId | |
483 | * @param firstResNum | |
484 | * @return | |
485 | */ | |
486 | 237 | protected void addSecondaryStructureAnnotation(String modelTitle, |
487 | SequenceI sq, char[] secstr, char[] secstrcode, String chainId, | |
488 | int firstResNum) | |
489 | { | |
490 | 237 | int length = sq.getLength(); |
491 | 237 | boolean ssFound = false; |
492 | 237 | Annotation asecstr[] = new Annotation[length |
493 | + (firstResNum - sq.getStart())]; | |
494 | 37915 | for (int p = 0; p < length; p++) |
495 | { | |
496 | 37678 | if (secstr[p] >= 'A' && secstr[p] <= 'z') |
497 | { | |
498 | 14640 | try |
499 | { | |
500 | 14640 | asecstr[p] = new Annotation(null, null, secstrcode[p], Float.NaN); |
501 | 14640 | ssFound = true; |
502 | } catch (Exception e) | |
503 | { | |
504 | // e.printStackTrace(); | |
505 | } | |
506 | } | |
507 | } | |
508 | ||
509 | 237 | if (ssFound) |
510 | { | |
511 | 215 | String mt = modelTitle == null ? getDataName() : modelTitle; |
512 | 215 | mt += chainId; |
513 | 215 | AlignmentAnnotation ann = new AlignmentAnnotation( |
514 | "Secondary Structure", "Secondary Structure for " + mt, | |
515 | asecstr); | |
516 | 215 | ann.belowAlignment = true; |
517 | 215 | ann.visible = true; |
518 | 215 | ann.autoCalculated = false; |
519 | 215 | ann.setCalcId(getClass().getName()); |
520 | 215 | ann.adjustForAlignment(); |
521 | 215 | ann.validateRangeAndDisplay(); |
522 | 215 | annotations.add(ann); |
523 | 215 | sq.addAlignmentAnnotation(ann); |
524 | } | |
525 | } | |
526 | ||
527 | 175 | private void waitForScript(Viewer jmd) |
528 | { | |
529 | 175 | while (jmd.isScriptExecuting()) |
530 | { | |
531 | 0 | try |
532 | { | |
533 | 0 | Thread.sleep(50); |
534 | ||
535 | } catch (InterruptedException x) | |
536 | { | |
537 | } | |
538 | } | |
539 | } | |
540 | ||
541 | /** | |
542 | * Convert Jmol's secondary structure code to Jalview's, and stored it in the | |
543 | * secondary structure arrays at the given sequence position | |
544 | * | |
545 | * @param proteinStructureSubType | |
546 | * @param pos | |
547 | * @param secstr | |
548 | * @param secstrcode | |
549 | */ | |
550 | 37684 | protected void setSecondaryStructure(STR proteinStructureSubType, int pos, |
551 | char[] secstr, char[] secstrcode) | |
552 | { | |
553 | 37684 | switch (proteinStructureSubType) |
554 | { | |
555 | 656 | case HELIX310: |
556 | 656 | secstr[pos] = '3'; |
557 | 656 | break; |
558 | 4177 | case HELIX: |
559 | 4872 | case HELIXALPHA: |
560 | 9049 | secstr[pos] = 'H'; |
561 | 9049 | break; |
562 | 1 | case HELIXPI: |
563 | 1 | secstr[pos] = 'P'; |
564 | 1 | break; |
565 | 5594 | case SHEET: |
566 | 5594 | secstr[pos] = 'E'; |
567 | 5594 | break; |
568 | 22384 | default: |
569 | 22384 | secstr[pos] = 0; |
570 | } | |
571 | ||
572 | 37684 | switch (proteinStructureSubType) |
573 | { | |
574 | 656 | case HELIX310: |
575 | 4872 | case HELIXALPHA: |
576 | 1 | case HELIXPI: |
577 | 4177 | case HELIX: |
578 | 9706 | secstrcode[pos] = 'H'; |
579 | 9706 | break; |
580 | 5594 | case SHEET: |
581 | 5594 | secstrcode[pos] = 'E'; |
582 | 5594 | break; |
583 | 22384 | default: |
584 | 22384 | secstrcode[pos] = 0; |
585 | } | |
586 | } | |
587 | ||
588 | /** | |
589 | * Convert any non-standard peptide codes to their standard code table | |
590 | * equivalent. (Initial version only does Selenomethionine MSE->MET.) | |
591 | * | |
592 | * @param threeLetterCode | |
593 | * @param seq | |
594 | * @param pos | |
595 | */ | |
596 | 0 | protected void replaceNonCanonicalResidue(String threeLetterCode, |
597 | char[] seq, int pos) | |
598 | { | |
599 | 0 | String canonical = ResidueProperties |
600 | .getCanonicalAminoAcid(threeLetterCode); | |
601 | 0 | if (canonical != null && !canonical.equalsIgnoreCase(threeLetterCode)) |
602 | { | |
603 | 0 | seq[pos] = ResidueProperties.getSingleCharacterCode(canonical); |
604 | } | |
605 | } | |
606 | ||
607 | /** | |
608 | * Not implemented - returns null | |
609 | */ | |
610 | 0 | @Override |
611 | public String print(SequenceI[] seqs, boolean jvSuffix) | |
612 | { | |
613 | 0 | return null; |
614 | } | |
615 | ||
616 | /** | |
617 | * Not implemented | |
618 | */ | |
619 | 0 | @Override |
620 | public void setCallbackFunction(String callbackType, | |
621 | String callbackFunction) | |
622 | { | |
623 | } | |
624 | ||
625 | 0 | @Override |
626 | public void notifyCallback(CBK cbType, Object[] data) | |
627 | { | |
628 | 0 | String strInfo = (data == null || data[1] == null ? null |
629 | : data[1].toString()); | |
630 | 0 | switch (cbType) |
631 | { | |
632 | 0 | case ECHO: |
633 | 0 | sendConsoleEcho(strInfo); |
634 | 0 | break; |
635 | 0 | case SCRIPT: |
636 | 0 | notifyScriptTermination((String) data[2], |
637 | ((Integer) data[3]).intValue()); | |
638 | 0 | break; |
639 | 0 | case MEASURE: |
640 | 0 | String mystatus = (String) data[3]; |
641 | 0 | if (mystatus.indexOf("Picked") >= 0 |
642 | || mystatus.indexOf("Sequence") >= 0) | |
643 | { | |
644 | // Picking mode | |
645 | 0 | sendConsoleMessage(strInfo); |
646 | } | |
647 | 0 | else if (mystatus.indexOf("Completed") >= 0) |
648 | { | |
649 | 0 | sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2, |
650 | strInfo.length() - 1)); | |
651 | } | |
652 | 0 | break; |
653 | 0 | case MESSAGE: |
654 | 0 | sendConsoleMessage(data == null ? null : strInfo); |
655 | 0 | break; |
656 | 0 | case PICK: |
657 | 0 | sendConsoleMessage(strInfo); |
658 | 0 | break; |
659 | 0 | default: |
660 | 0 | break; |
661 | } | |
662 | } | |
663 | ||
664 | String lastConsoleEcho = ""; | |
665 | ||
666 | 0 | private void sendConsoleEcho(String string) |
667 | { | |
668 | 0 | lastConsoleEcho += string; |
669 | 0 | lastConsoleEcho += "\n"; |
670 | } | |
671 | ||
672 | String lastConsoleMessage = ""; | |
673 | ||
674 | 0 | private void sendConsoleMessage(String string) |
675 | { | |
676 | 0 | lastConsoleMessage += string; |
677 | 0 | lastConsoleMessage += "\n"; |
678 | } | |
679 | ||
680 | int lastScriptTermination = -1; | |
681 | ||
682 | String lastScriptMessage = ""; | |
683 | ||
684 | 0 | private void notifyScriptTermination(String string, int intValue) |
685 | { | |
686 | 0 | lastScriptMessage += string; |
687 | 0 | lastScriptMessage += "\n"; |
688 | 0 | lastScriptTermination = intValue; |
689 | } | |
690 | ||
691 | 0 | @Override |
692 | public boolean notifyEnabled(CBK callbackPick) | |
693 | { | |
694 | 0 | switch (callbackPick) |
695 | { | |
696 | 0 | case MESSAGE: |
697 | 0 | case SCRIPT: |
698 | 0 | case ECHO: |
699 | 0 | case LOADSTRUCT: |
700 | 0 | case ERROR: |
701 | 0 | return true; |
702 | 0 | default: |
703 | 0 | return false; |
704 | } | |
705 | } | |
706 | ||
707 | /** | |
708 | * Not implemented - returns null | |
709 | */ | |
710 | 0 | @Override |
711 | public String eval(String strEval) | |
712 | { | |
713 | 0 | return null; |
714 | } | |
715 | ||
716 | /** | |
717 | * Not implemented - returns null | |
718 | */ | |
719 | 0 | @Override |
720 | public float[][] functionXY(String functionName, int x, int y) | |
721 | { | |
722 | 0 | return null; |
723 | } | |
724 | ||
725 | /** | |
726 | * Not implemented - returns null | |
727 | */ | |
728 | 0 | @Override |
729 | public float[][][] functionXYZ(String functionName, int nx, int ny, | |
730 | int nz) | |
731 | { | |
732 | 0 | return null; |
733 | } | |
734 | ||
735 | /** | |
736 | * Not implemented - returns null | |
737 | */ | |
738 | 0 | @Override |
739 | public String createImage(String fileName, String imageType, | |
740 | Object text_or_bytes, int quality) | |
741 | { | |
742 | 0 | return null; |
743 | } | |
744 | ||
745 | /** | |
746 | * Not implemented - returns null | |
747 | */ | |
748 | 0 | @Override |
749 | public Map<String, Object> getRegistryInfo() | |
750 | { | |
751 | 0 | return null; |
752 | } | |
753 | ||
754 | /** | |
755 | * Not implemented | |
756 | */ | |
757 | 0 | @Override |
758 | public void showUrl(String url) | |
759 | { | |
760 | } | |
761 | ||
762 | /** | |
763 | * Not implemented - returns null | |
764 | */ | |
765 | 0 | @Override |
766 | public int[] resizeInnerPanel(String data) | |
767 | { | |
768 | 0 | return null; |
769 | } | |
770 | ||
771 | 0 | @Override |
772 | public Map<String, Object> getJSpecViewProperty(String arg0) | |
773 | { | |
774 | 0 | return null; |
775 | } | |
776 | ||
777 | 0 | public boolean isPredictSecondaryStructure() |
778 | { | |
779 | 0 | return predictSecondaryStructure; |
780 | } | |
781 | ||
782 | 0 | public void setPredictSecondaryStructure( |
783 | boolean predictSecondaryStructure) | |
784 | { | |
785 | 0 | this.predictSecondaryStructure = predictSecondaryStructure; |
786 | } | |
787 | ||
788 | 0 | public boolean isVisibleChainAnnotation() |
789 | { | |
790 | 0 | return visibleChainAnnotation; |
791 | } | |
792 | ||
793 | 0 | public void setVisibleChainAnnotation(boolean visibleChainAnnotation) |
794 | { | |
795 | 0 | this.visibleChainAnnotation = visibleChainAnnotation; |
796 | } | |
797 | ||
798 | } |