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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 mc_view; | |
22 | ||
23 | import java.awt.Color; | |
24 | import java.util.List; | |
25 | import java.util.Locale; | |
26 | import java.util.Vector; | |
27 | ||
28 | import jalview.analysis.AlignSeq; | |
29 | import jalview.datamodel.AlignmentAnnotation; | |
30 | import jalview.datamodel.Annotation; | |
31 | import jalview.datamodel.ContactMatrixI; | |
32 | import jalview.datamodel.Mapping; | |
33 | import jalview.datamodel.Sequence; | |
34 | import jalview.datamodel.SequenceFeature; | |
35 | import jalview.datamodel.SequenceI; | |
36 | import jalview.datamodel.annotations.AnnotationRowBuilder; | |
37 | import jalview.schemes.ColourSchemeI; | |
38 | import jalview.schemes.ResidueProperties; | |
39 | import jalview.structure.StructureImportSettings; | |
40 | import jalview.structure.StructureMapping; | |
41 | import jalview.util.Comparison; | |
42 | import jalview.ws.datamodel.MappableContactMatrixI; | |
43 | ||
44 | public class PDBChain | |
45 | { | |
46 | public static final String RESNUM_FEATURE = "RESNUM"; | |
47 | ||
48 | private static final String IEASTATUS = "IEA:jalview"; | |
49 | ||
50 | public String id; | |
51 | ||
52 | public Vector<Bond> bonds = new Vector<>(); | |
53 | ||
54 | public Vector<Atom> atoms = new Vector<>(); | |
55 | ||
56 | public Vector<Residue> residues = new Vector<>(); | |
57 | ||
58 | public int offset; | |
59 | ||
60 | /** | |
61 | * sequence is the sequence extracted by the chain parsing code | |
62 | */ | |
63 | public SequenceI sequence; | |
64 | ||
65 | /** | |
66 | * shadow is the sequence created by any other parsing processes (e.g. Jmol, | |
67 | * RNAview) | |
68 | */ | |
69 | public SequenceI shadow = null; | |
70 | ||
71 | public boolean isNa = false; | |
72 | ||
73 | public boolean isVisible = true; | |
74 | ||
75 | public int pdbstart = 0; | |
76 | ||
77 | public int pdbend = 0; | |
78 | ||
79 | public int seqstart = 0; | |
80 | ||
81 | public int seqend = 0; | |
82 | ||
83 | public String pdbid = ""; | |
84 | ||
85 | AnnotationRowBuilder tfacTemplate = new AnnotationRowBuilder( | |
86 | "Temperature Factor"); | |
87 | ||
88 | 267 | public PDBChain(String thePdbid, String theId, |
89 | AnnotationRowBuilder template) | |
90 | { | |
91 | 267 | this(thePdbid, theId); |
92 | 267 | if (template != null) |
93 | { | |
94 | 34 | tfacTemplate = template; |
95 | } | |
96 | } | |
97 | ||
98 | /** | |
99 | * import chain data assuming Temperature Factor is in the Temperature Factor | |
100 | * column | |
101 | * | |
102 | * @param thePdbid | |
103 | * @param theId | |
104 | */ | |
105 | 314 | public PDBChain(String thePdbid, String theId) |
106 | { | |
107 | 314 | this.pdbid = thePdbid == null ? thePdbid |
108 | : thePdbid.toLowerCase(Locale.ROOT); | |
109 | 314 | this.id = theId; |
110 | } | |
111 | ||
112 | /** | |
113 | * character used to write newlines | |
114 | */ | |
115 | protected String newline = System.getProperty("line.separator"); | |
116 | ||
117 | public Mapping shadowMap; | |
118 | ||
119 | 1 | public void setNewlineString(String nl) |
120 | { | |
121 | 1 | newline = nl; |
122 | } | |
123 | ||
124 | 2 | public String getNewlineString() |
125 | { | |
126 | 2 | return newline; |
127 | } | |
128 | ||
129 | 1 | public String print() |
130 | { | |
131 | 1 | StringBuilder tmp = new StringBuilder(256); |
132 | ||
133 | 1 | for (Bond b : bonds) |
134 | { | |
135 | 3 | tmp.append(b.at1.resName).append(" ").append(b.at1.resNumber) |
136 | .append(" ").append(offset).append(newline); | |
137 | } | |
138 | ||
139 | 1 | return tmp.toString(); |
140 | } | |
141 | ||
142 | /** | |
143 | * Annotate the residues with their corresponding positions in s1 using the | |
144 | * alignment in as NOTE: This clears all atom.alignmentMapping values on the | |
145 | * structure. | |
146 | * | |
147 | * @param as | |
148 | * @param s1 | |
149 | */ | |
150 | 194 | public void makeExactMapping(AlignSeq as, SequenceI s1) |
151 | { | |
152 | 194 | int pdbpos = as.getSeq2Start() - 2; |
153 | 194 | int alignpos = s1.getStart() + as.getSeq1Start() - 3; |
154 | // first clear out any old alignmentMapping values: | |
155 | 194 | for (Atom atom : atoms) |
156 | { | |
157 | 21216 | atom.alignmentMapping = -1; |
158 | } | |
159 | // and now trace the alignment onto the atom set. | |
160 | 21403 | for (int i = 0; i < as.astr1.length(); i++) |
161 | { | |
162 | 21209 | if (as.astr1.charAt(i) != '-') |
163 | { | |
164 | 21209 | alignpos++; |
165 | } | |
166 | ||
167 | 21209 | if (as.astr2.charAt(i) != '-') |
168 | { | |
169 | 21209 | pdbpos++; |
170 | } | |
171 | ||
172 | 21209 | boolean sameResidue = Comparison.isSameResidue(as.astr1.charAt(i), |
173 | as.astr2.charAt(i), false); | |
174 | 21209 | if (sameResidue) |
175 | { | |
176 | 21164 | if (pdbpos >= residues.size()) |
177 | { | |
178 | 0 | continue; |
179 | } | |
180 | 21164 | Residue res = residues.elementAt(pdbpos); |
181 | 21164 | for (Atom atom : res.atoms) |
182 | { | |
183 | 21167 | atom.alignmentMapping = alignpos; |
184 | } | |
185 | } | |
186 | } | |
187 | } | |
188 | ||
189 | /** | |
190 | * Annotate the residues with their corresponding positions in s1 using the | |
191 | * alignment in as NOTE: This clears all atom.alignmentMapping values on the | |
192 | * structure. | |
193 | * | |
194 | * @param as | |
195 | * @param s1 | |
196 | */ | |
197 | 0 | public void makeExactMapping(StructureMapping mapping, SequenceI s1) |
198 | { | |
199 | // first clear out any old alignmentMapping values: | |
200 | 0 | for (Atom atom : atoms) |
201 | { | |
202 | 0 | atom.alignmentMapping = -1; |
203 | } | |
204 | 0 | SequenceI ds = s1; |
205 | 0 | while (ds.getDatasetSequence() != null) |
206 | { | |
207 | 0 | ds = ds.getDatasetSequence(); |
208 | } | |
209 | 0 | int pdboffset = 0; |
210 | 0 | for (Residue res : residues) |
211 | { | |
212 | // res.number isn't set correctly for discontinuous/mismapped residues | |
213 | 0 | int seqpos = mapping.getSeqPos(res.atoms.get(0).resNumber); |
214 | 0 | char strchar = sequence.getCharAt(pdboffset++); |
215 | 0 | if (seqpos == StructureMapping.UNASSIGNED_VALUE) |
216 | { | |
217 | 0 | continue; |
218 | } | |
219 | 0 | char seqchar = ds.getCharAt(seqpos - ds.getStart()); |
220 | ||
221 | 0 | boolean sameResidue = Comparison.isSameResidue(seqchar, strchar, |
222 | false); | |
223 | 0 | if (sameResidue) |
224 | { | |
225 | 0 | for (Atom atom : res.atoms) |
226 | { | |
227 | 0 | atom.alignmentMapping = seqpos - 1; |
228 | } | |
229 | } | |
230 | } | |
231 | } | |
232 | ||
233 | /** | |
234 | * Copies over the RESNUM seqfeatures from the internal chain sequence to the | |
235 | * mapped sequence | |
236 | * | |
237 | * @param seq | |
238 | * @param status | |
239 | * The Status of the transferred annotation | |
240 | * | |
241 | * @param altPDBID | |
242 | * the group id for the features on the destination sequence (e.g. | |
243 | * the official accession ID) | |
244 | */ | |
245 | 193 | public void transferRESNUMFeatures(SequenceI seq, String status, |
246 | String altPDBID) | |
247 | { | |
248 | 193 | if (altPDBID == null) |
249 | { | |
250 | 0 | altPDBID = pdbid; |
251 | } | |
252 | 193 | SequenceI sq = seq; |
253 | 384 | while (sq != null && sq.getDatasetSequence() != null) |
254 | { | |
255 | 191 | sq = sq.getDatasetSequence(); |
256 | 191 | if (sq == sequence) |
257 | { | |
258 | 0 | return; |
259 | } | |
260 | } | |
261 | ||
262 | /* | |
263 | * Remove any existing features for this chain if they exist ? | |
264 | * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int | |
265 | * totfeat=seqsfeatures.length; // Remove any features for this exact chain | |
266 | * ? for (int i=0; i<seqsfeatures.length; i++) { } | |
267 | */ | |
268 | 193 | if (status == null) |
269 | { | |
270 | 193 | status = PDBChain.IEASTATUS; |
271 | } | |
272 | ||
273 | 193 | List<SequenceFeature> features = sequence.getSequenceFeatures(); |
274 | 193 | for (SequenceFeature feature : features) |
275 | { | |
276 | 21210 | if (feature.getFeatureGroup() != null |
277 | && feature.getFeatureGroup().equals(pdbid)) | |
278 | { | |
279 | 21210 | int newBegin = 1 |
280 | + residues.elementAt(feature.getBegin() - offset).atoms | |
281 | .elementAt(0).alignmentMapping; | |
282 | 21210 | int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms |
283 | .elementAt(0).alignmentMapping; | |
284 | 21210 | SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd, |
285 | altPDBID, feature.getScore()); | |
286 | 21210 | tx.setStatus(status |
287 | 21210 | + ((tx.getStatus() == null || tx.getStatus().length() == 0) |
288 | ? "" | |
289 | : ":" + tx.getStatus())); | |
290 | 21210 | if (tx.begin != 0 && tx.end != 0) |
291 | { | |
292 | 21161 | sq.addSequenceFeature(tx); |
293 | } | |
294 | } | |
295 | } | |
296 | } | |
297 | ||
298 | /** | |
299 | * Traverses the list of residues and constructs bonds where CA-to-CA atoms or | |
300 | * P-to-P atoms are found. Also sets the 'isNa' flag if more than 99% of | |
301 | * residues contain a P not a CA. | |
302 | */ | |
303 | 304 | public void makeCaBondList() |
304 | { | |
305 | 304 | boolean na = false; |
306 | 304 | int numNa = 0; |
307 | 48051 | for (int i = 0; i < (residues.size() - 1); i++) |
308 | { | |
309 | 47747 | Residue tmpres = residues.elementAt(i); |
310 | 47747 | Residue tmpres2 = residues.elementAt(i + 1); |
311 | 47747 | Atom at1 = tmpres.findAtom("CA"); |
312 | 47747 | Atom at2 = tmpres2.findAtom("CA"); |
313 | 47747 | na = false; |
314 | 47747 | if ((at1 == null) && (at2 == null)) |
315 | { | |
316 | 2 | na = true; |
317 | 2 | at1 = tmpres.findAtom("P"); |
318 | 2 | at2 = tmpres2.findAtom("P"); |
319 | } | |
320 | 47747 | if ((at1 != null) && (at2 != null)) |
321 | { | |
322 | 47747 | if (at1.chain.equals(at2.chain)) |
323 | { | |
324 | 47747 | if (na) |
325 | { | |
326 | 2 | numNa++; |
327 | } | |
328 | 47747 | makeBond(at1, at2); |
329 | } | |
330 | } | |
331 | else | |
332 | { | |
333 | 0 | System.out.println("not found " + i); |
334 | } | |
335 | } | |
336 | ||
337 | /* | |
338 | * If > 99% 'P', flag as nucleotide; note the count doesn't include the last | |
339 | * residue | |
340 | */ | |
341 | 304 | if (residues.size() > 1 && (numNa / (residues.size() - 1) > 0.99)) |
342 | { | |
343 | 1 | isNa = true; |
344 | } | |
345 | } | |
346 | ||
347 | /** | |
348 | * Construct a bond from atom1 to atom2 and add it to the list of bonds for | |
349 | * this chain | |
350 | * | |
351 | * @param at1 | |
352 | * @param at2 | |
353 | */ | |
354 | 47757 | public void makeBond(Atom at1, Atom at2) |
355 | { | |
356 | 47757 | bonds.addElement(new Bond(at1, at2)); |
357 | } | |
358 | ||
359 | /** | |
360 | * Traverses the list of atoms and | |
361 | * <ul> | |
362 | * <li>constructs a list of Residues, each containing all the atoms that share | |
363 | * the same residue number</li> | |
364 | * <li>adds a RESNUM sequence feature for each position</li> | |
365 | * <li>creates the sequence string</li> | |
366 | * <li>determines if nucleotide</li> | |
367 | * <li>saves the residue number of the first atom as 'offset'</li> | |
368 | * <li>adds temp factor annotation if the flag is set to do so</li> | |
369 | * </ul> | |
370 | * | |
371 | * @param visibleChainAnnotation | |
372 | */ | |
373 | 307 | public void makeResidueList(boolean visibleChainAnnotation) |
374 | { | |
375 | 307 | int count = 0; |
376 | 307 | Object symbol; |
377 | 307 | boolean deoxyn = false; |
378 | 307 | boolean nucleotide = false; |
379 | 307 | StringBuilder seq = new StringBuilder(256); |
380 | 307 | Vector<SequenceFeature> resFeatures = new Vector<>(); |
381 | 307 | Vector<Annotation> resAnnotation = new Vector<>(); |
382 | 307 | int iSize = atoms.size() - 1; |
383 | 307 | int resNumber = -1; |
384 | 307 | char insCode = ' '; |
385 | ||
386 | 48367 | for (int i = 0; i <= iSize; i++) |
387 | { | |
388 | 48060 | Atom tmp = atoms.elementAt(i); |
389 | 48060 | resNumber = tmp.resNumber; |
390 | 48060 | insCode = tmp.insCode; |
391 | ||
392 | 48060 | int res = resNumber; |
393 | 48060 | char ins = insCode; |
394 | ||
395 | 48060 | if (i == 0) |
396 | { | |
397 | 307 | offset = resNumber; |
398 | } | |
399 | ||
400 | 48060 | Vector<Atom> resAtoms = new Vector<>(); |
401 | // Add atoms to a vector while the residue number | |
402 | // remains the same as the first atom's resNumber (res) | |
403 | 96141 | while ((resNumber == res) && (ins == insCode) && (i < atoms.size())) |
404 | { | |
405 | 48081 | resAtoms.add(atoms.elementAt(i)); |
406 | 48081 | i++; |
407 | ||
408 | 48081 | if (i < atoms.size()) |
409 | { | |
410 | 47774 | resNumber = atoms.elementAt(i).resNumber; |
411 | 47774 | insCode = atoms.elementAt(i).insCode; |
412 | } | |
413 | else | |
414 | { | |
415 | 307 | resNumber++; |
416 | } | |
417 | } | |
418 | ||
419 | // We need this to keep in step with the outer for i = loop | |
420 | 48060 | i--; |
421 | ||
422 | // Add inserted residues as features to the base residue | |
423 | 48060 | Atom currAtom = resAtoms.get(0); |
424 | 48060 | if (currAtom.insCode != ' ' && !residues.isEmpty() |
425 | && residues.lastElement().atoms | |
426 | .get(0).resNumber == currAtom.resNumber) | |
427 | { | |
428 | 0 | String desc = currAtom.resName + ":" + currAtom.resNumIns + " " |
429 | + pdbid + id; | |
430 | 0 | SequenceFeature sf = new SequenceFeature("INSERTION", desc, |
431 | offset + count - 1, offset + count - 1, "PDB_INS"); | |
432 | 0 | resFeatures.addElement(sf); |
433 | 0 | residues.lastElement().atoms.addAll(resAtoms); |
434 | } | |
435 | else | |
436 | { | |
437 | // Make a new Residue object with the new atoms vector | |
438 | 48060 | residues.addElement(new Residue(resAtoms, resNumber - 1, count)); |
439 | ||
440 | 48060 | Residue tmpres = residues.lastElement(); |
441 | 48060 | Atom tmpat = tmpres.atoms.get(0); |
442 | // Make A new SequenceFeature for the current residue numbering | |
443 | 48060 | String desc = tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid |
444 | + id; | |
445 | 48060 | SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc, |
446 | offset + count, offset + count, pdbid); | |
447 | 48060 | resFeatures.addElement(sf); |
448 | 48060 | resAnnotation.addElement(new Annotation(tmpat.tfactor)); |
449 | // Keep totting up the sequence | |
450 | ||
451 | ? | if ((symbol = ResidueProperties.getAA3Hash() |
452 | .get(tmpat.resName)) == null) | |
453 | { | |
454 | 7 | String nucname = tmpat.resName.trim(); |
455 | // use the aaIndex rather than call 'toLower' - which would take a bit | |
456 | // more time. | |
457 | 7 | deoxyn = nucname.length() == 2 |
458 | && ResidueProperties.aaIndex[nucname | |
459 | .charAt(0)] == ResidueProperties.aaIndex['D']; | |
460 | 7 | if (tmpat.name.equalsIgnoreCase("CA") |
461 | || ResidueProperties.nucleotideIndex[nucname | |
462 | 3 | .charAt((deoxyn ? 1 : 0))] == -1) |
463 | { | |
464 | 4 | char r = ResidueProperties.getSingleCharacterCode( |
465 | ResidueProperties.getCanonicalAminoAcid(tmpat.resName)); | |
466 | 4 | seq.append(r == '0' ? 'X' : r); |
467 | // System.err.println("PDBReader:Null aa3Hash for " + | |
468 | // tmpat.resName); | |
469 | } | |
470 | else | |
471 | { | |
472 | // nucleotide flag | |
473 | 3 | nucleotide = true; |
474 | 3 | seq.append(nucname.charAt((deoxyn ? 1 : 0))); |
475 | } | |
476 | } | |
477 | else | |
478 | { | |
479 | 48053 | if (nucleotide) |
480 | { | |
481 | 0 | System.err.println( |
482 | "Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!"); | |
483 | } | |
484 | 48053 | seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]); |
485 | } | |
486 | 48060 | count++; |
487 | } | |
488 | } | |
489 | ||
490 | 307 | if (id.length() < 1) |
491 | { | |
492 | 0 | id = " "; |
493 | } | |
494 | 307 | isNa = nucleotide; |
495 | 307 | sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note: |
496 | // resNumber-offset | |
497 | // ~= | |
498 | // seq.size() | |
499 | // Add normalised feature scores to RESNUM indicating start/end of sequence | |
500 | // sf.setScore(offset+count); | |
501 | ||
502 | // System.out.println("PDB Sequence is :\nSequence = " + seq); | |
503 | // System.out.println("No of residues = " + residues.size()); | |
504 | ||
505 | 307 | if (StructureImportSettings.isShowSeqFeatures()) |
506 | { | |
507 | 293 | iSize = resFeatures.size(); |
508 | 45001 | for (int i = 0; i < iSize; i++) |
509 | { | |
510 | 44708 | sequence.addSequenceFeature(resFeatures.elementAt(i)); |
511 | 44708 | resFeatures.setElementAt(null, i); |
512 | } | |
513 | } | |
514 | 307 | if (visibleChainAnnotation) |
515 | { | |
516 | 203 | Annotation[] annots = new Annotation[resAnnotation.size()]; |
517 | 203 | float max = 0f; |
518 | 203 | float min = 0f; |
519 | 203 | iSize = annots.length; |
520 | 33539 | for (int i = 0; i < iSize; i++) |
521 | { | |
522 | 33336 | annots[i] = resAnnotation.elementAt(i); |
523 | 33336 | tfacTemplate.processAnnotation(annots[i]); |
524 | 33336 | max = Math.max(max, annots[i].value); |
525 | 33336 | min = Math.min(min, annots[i].value); |
526 | 33336 | resAnnotation.setElementAt(null, i); |
527 | } | |
528 | 203 | if (tfacTemplate.isHasMinMax()) |
529 | { | |
530 | 27 | max = tfacTemplate.getMax(); |
531 | 27 | min = tfacTemplate.getMin(); |
532 | } | |
533 | ||
534 | 203 | AlignmentAnnotation tfactorann = new AlignmentAnnotation( |
535 | tfacTemplate.getName(), | |
536 | 203 | (tfacTemplate.isHasDescription() |
537 | ? tfacTemplate.getDescription() | |
538 | : tfacTemplate.getName()) + " for " + pdbid + id, | |
539 | annots, min, max, AlignmentAnnotation.LINE_GRAPH); | |
540 | 203 | tfactorann.setTFType(tfacTemplate.getTFType()); |
541 | 203 | tfactorann.setCalcId(getClass().getName()); |
542 | ||
543 | 203 | tfactorann.setSequenceRef(sequence); |
544 | 203 | sequence.addAlignmentAnnotation(tfactorann); |
545 | } | |
546 | } | |
547 | ||
548 | /** | |
549 | * Colour start/end of bonds by charge | |
550 | * <ul> | |
551 | * <li>ASP and GLU red</li> | |
552 | * <li>LYS and ARG blue</li> | |
553 | * <li>CYS yellow</li> | |
554 | * <li>others light gray</li> | |
555 | * </ul> | |
556 | */ | |
557 | 1 | public void setChargeColours() |
558 | { | |
559 | 1 | for (Bond b : bonds) |
560 | { | |
561 | 3 | if (b.at1 != null && b.at2 != null) |
562 | { | |
563 | 3 | b.startCol = getChargeColour(b.at1.resName); |
564 | 3 | b.endCol = getChargeColour(b.at2.resName); |
565 | } | |
566 | else | |
567 | { | |
568 | 0 | b.startCol = Color.gray; |
569 | 0 | b.endCol = Color.gray; |
570 | } | |
571 | } | |
572 | } | |
573 | ||
574 | 13 | public static Color getChargeColour(String resName) |
575 | { | |
576 | 13 | Color result = Color.lightGray; |
577 | 13 | if ("ASP".equals(resName) || "GLU".equals(resName)) |
578 | { | |
579 | 3 | result = Color.red; |
580 | } | |
581 | 10 | else if ("LYS".equals(resName) || "ARG".equals(resName)) |
582 | { | |
583 | 4 | result = Color.blue; |
584 | } | |
585 | 6 | else if ("CYS".equals(resName)) |
586 | { | |
587 | 3 | result = Color.yellow; |
588 | } | |
589 | 13 | return result; |
590 | } | |
591 | ||
592 | /** | |
593 | * Sets the start/end colours of bonds to those of the start/end atoms | |
594 | * according to the specified colour scheme. Note: currently only works for | |
595 | * peptide residues. | |
596 | * | |
597 | * @param cs | |
598 | */ | |
599 | 1 | public void setChainColours(ColourSchemeI cs) |
600 | { | |
601 | 1 | int index; |
602 | 1 | for (Bond b : bonds) |
603 | { | |
604 | 3 | try |
605 | { | |
606 | 3 | index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue(); |
607 | 3 | b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0, |
608 | null, null, 0f); | |
609 | ||
610 | 3 | index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue(); |
611 | 2 | b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0, |
612 | null, null, 0f); | |
613 | ||
614 | } catch (Exception e) | |
615 | { | |
616 | 1 | b.startCol = Color.gray; |
617 | 1 | b.endCol = Color.gray; |
618 | } | |
619 | } | |
620 | } | |
621 | ||
622 | 1 | public void setChainColours(Color col) |
623 | { | |
624 | 1 | for (Bond b : bonds) |
625 | { | |
626 | 2 | b.startCol = col; |
627 | 2 | b.endCol = col; |
628 | } | |
629 | } | |
630 | ||
631 | /** | |
632 | * copy any sequence annotation onto the sequence mapped using the provided | |
633 | * StructureMapping | |
634 | * | |
635 | * @param mapping | |
636 | * - positional mapping between destination sequence and pdb resnum | |
637 | * @param sqmpping | |
638 | * - mapping between destination sequence and local chain | |
639 | */ | |
640 | 193 | public void transferResidueAnnotation(StructureMapping mapping, |
641 | jalview.datamodel.Mapping sqmpping) | |
642 | { | |
643 | 193 | SequenceI sq = mapping.getSequence(); |
644 | 193 | SequenceI dsq = sq; |
645 | 193 | if (sqmpping == null) |
646 | { | |
647 | // SIFTS mappings are recorded in the StructureMapping object... | |
648 | ||
649 | 0 | sqmpping = mapping.getSeqToPdbMapping(); |
650 | } | |
651 | 193 | if (sq != null) |
652 | { | |
653 | 384 | while (dsq.getDatasetSequence() != null) |
654 | { | |
655 | 191 | dsq = dsq.getDatasetSequence(); |
656 | } | |
657 | // any annotation will be transferred onto the dataset sequence | |
658 | ||
659 | 193 | if (shadow != null && shadow.getAnnotation() != null) |
660 | { | |
661 | ||
662 | 0 | for (AlignmentAnnotation ana : shadow.getAnnotation()) |
663 | { | |
664 | // match on calcId, label and description so annotations from | |
665 | // different structures are preserved | |
666 | 0 | List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations( |
667 | ana.getCalcId(), ana.label, ana.description); | |
668 | 0 | if (transfer == null || transfer.size() == 0) |
669 | { | |
670 | 0 | ContactMatrixI cm = shadow.getContactMatrixFor(ana); |
671 | 0 | ana = new AlignmentAnnotation(ana); |
672 | // TODO map contact matrix under mapping | |
673 | 0 | ana.liftOver(sequence, shadowMap); |
674 | 0 | ana.liftOver(dsq, sqmpping); |
675 | 0 | dsq.addAlignmentAnnotation(ana); |
676 | 0 | if (cm != null) |
677 | { | |
678 | 0 | dsq.addContactListFor(ana, cm); |
679 | } | |
680 | } | |
681 | else | |
682 | { | |
683 | 0 | continue; |
684 | } | |
685 | } | |
686 | } | |
687 | else | |
688 | { | |
689 | 193 | if (sequence != null && sequence.getAnnotation() != null) |
690 | { | |
691 | 154 | for (AlignmentAnnotation ana : sequence.getAnnotation()) |
692 | { | |
693 | // match on calcId, label and description so annotations from | |
694 | // different structures are preserved | |
695 | 335 | List<AlignmentAnnotation> transfer = dsq |
696 | .getAlignmentAnnotations(ana.getCalcId(), ana.label, | |
697 | ana.description); | |
698 | 335 | if (transfer == null || transfer.size() == 0) |
699 | { | |
700 | 177 | ContactMatrixI cm = sequence.getContactMatrixFor(ana); |
701 | 177 | ana = new AlignmentAnnotation(ana); |
702 | 177 | ana.liftOver(dsq, sqmpping); |
703 | 177 | dsq.addAlignmentAnnotation(ana); |
704 | 177 | if (cm != null && cm instanceof MappableContactMatrixI) |
705 | { | |
706 | 36 | dsq.addContactListFor(ana, ((MappableContactMatrixI) cm) |
707 | .liftOver(dsq, sqmpping)); | |
708 | } | |
709 | } | |
710 | else | |
711 | { | |
712 | 158 | continue; |
713 | } | |
714 | } | |
715 | } | |
716 | } | |
717 | 193 | if (false) |
718 | { | |
719 | // Useful for debugging mappings - adds annotation for mapped position | |
720 | 0 | float min = -1, max = 0; |
721 | 0 | Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1]; |
722 | 0 | for (int i = sq.getStart(), j = sq |
723 | 0 | .getEnd(), k = 0; i <= j; i++, k++) |
724 | { | |
725 | 0 | int prn = mapping.getPDBResNum(k + 1); |
726 | ||
727 | 0 | an[k] = new Annotation(prn); |
728 | 0 | if (min == -1) |
729 | { | |
730 | 0 | min = k; |
731 | 0 | max = k; |
732 | } | |
733 | else | |
734 | { | |
735 | 0 | if (min > k) |
736 | { | |
737 | 0 | min = k; |
738 | } | |
739 | 0 | else if (max < k) |
740 | { | |
741 | 0 | max = k; |
742 | } | |
743 | } | |
744 | } | |
745 | 0 | sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM", |
746 | "PDB Residue Numbering for " + this.pdbid + ":" + this.id, | |
747 | an, min, max, AlignmentAnnotation.LINE_GRAPH)); | |
748 | } | |
749 | } | |
750 | } | |
751 | } |