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source/XpertMassCore/src/
File: source/XpertMassCore/src/PolChemDef.cpp
Date: 2025-11-20 01:41:33
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1 /* BEGIN software license
2 *
3 * MsXpertSuite - mass spectrometry software suite
4 * -----------------------------------------------
5 * Copyright(C) 2009,...,2018 Filippo Rusconi
6 *
7 * http://www.msxpertsuite.org
8 *
9 * This file is part of the MsXpertSuite project.
10 *
11 * The MsXpertSuite project is the successor of the massXpert project. This
12 * project now includes various independent modules:
13 *
14 * - massXpert, model polymer chemistries and simulate mass spectrometric data;
15 * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
16 *
17 * This program is free software: you can redistribute it and/or modify
18 * it under the terms of the GNU General Public License as published by
19 * the Free Software Foundation, either version 3 of the License, or
20 * (at your option) any later version.
21 *
22 * This program is distributed in the hope that it will be useful,
23 * but WITHOUT ANY WARRANTY; without even the implied warranty of
24 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
25 * GNU General Public License for more details.
26 *
27 * You should have received a copy of the GNU General Public License
28 * along with this program. If not, see <http://www.gnu.org/licenses/>.
29 *
30 * END software license
31 */
32
33
34 ////////////////////////////// Stdlib includes
35 #include <map>
36 #include <vector>
37
38 /////////////////////// Qt includes
39 #include <QDebug>
40 #include <QFileInfo>
41 #include <QDir>
42
43
44 /////////////////////// Local includes
45 #include "MsXpS/libXpertMassCore/PolChemDef.hpp"
46 #include "MsXpS/libXpertMassCore/Monomer.hpp"
47 #include "MsXpS/libXpertMassCore/CrossLinker.hpp"
48 #include "MsXpS/libXpertMassCore/CleavageAgent.hpp"
49 #include "MsXpS/libXpertMassCore/FragmentationPathway.hpp"
50 #include "MsXpS/libXpertMassCore/IsotopicDataLibraryHandler.hpp"
51 #include "MsXpS/libXpertMassCore/IsotopicDataUserConfigHandler.hpp"
52
53
54 int polChemDefSPtrMetaTypeId =
55 qRegisterMetaType<MsXpS::libXpertMassCore::PolChemDefSPtr>("PolChemDefSPtr");
56
57 int polChemDefCstSPtrMetaTypeId =
58 qRegisterMetaType<MsXpS::libXpertMassCore::PolChemDefCstSPtr>(
59 "PolChemDefCstSPtr");
60
61 namespace MsXpS
62 {
63 namespace libXpertMassCore
64 {
65
66 /*!
67 \class MsXpS::libXpertMassCore::PolChemDef
68 \inmodule libXpertMassCore
69 \ingroup PolChemDef
70 \inheaderfile PolChemDef.hpp
71
72 \brief The PolChemDef class provides a complete set of chemical entities
73 fully qualifying a polymer chemistry definition, like Proteins, Saccharides or
74 Nucleic acids.
75
76 The PolChemDef class provides a full set of chemical entity definitions
77 (\l{Isotope}s, \l{Monomer}s, chemical \l{Modif}ications, \l{CrossLink}s),
78 chemical reaction models (in the liquid or gas phase, like \l Polymer cleavage:
79 \l CleavageAgent or \l Oligomer fragmentation: \l FragmentationPathway)\dots
80 */
81
82 /*!
83 \variable MsXpS::libXpertMassCore::PolChemDef::m_name
84
85 \brief The name of the polymer chemistry definition, like \e{protein-1-letter}
86 or \e{nucac}, for example.
87
88 This name is typically identical to both the name of the directory where all
89 the data defining this \c PolChemDef is stored and the name of the XML file
90 that contains the definition itself.
91 */
92
93 /*!
94 \variable MsXpS::libXpertMassCore::PolChemDef::m_xmlDataFilePath
95
96 \brief The path to the XML data file that contains the description of this
97 polymer chemistry definition.
98 */
99
100
101 /*!
102 \variable MsXpS::libXpertMassCore::PolChemDef::m_isotopicDataFilePath
103
104 \brief The path to the file that contains this polymer chemistry definition's
105 isotopic data.
106 */
107
108 /*!
109 \variable MsXpS::libXpertMassCore::PolChemDef::m_leftCap
110
111 \brief The \l Formula that defines how of the left end of a polymer
112 sequence of this \l PolChemDef needs to be capped in order to finalize the
113 polymerization state of the \l Polymer sequence.
114
115 \sa PolChemDef::m_rightCap
116 */
117
118 /*!
119 \variable MsXpS::libXpertMassCore::PolChemDef::m_rightCap
120
121 \brief The \l Formula that defines how of the right end of a polymer
122 sequence of this \l PolChemDef needs to be capped in order to finalize the
123 polymerization state of the \l Polymer sequence.
124
125 \sa PolChemDef::m_leftCap
126 */
127
128 /*!
129 \variable MsXpS::libXpertMassCore::PolChemDef::m_codeLength
130
131 \brief The maximum length of a \l Monomer code in this defintion.
132
133 The valid syntax of a Monomer code is that the first character of the code is
134 uppercase and all the remaining ones are lowercase. The total number of
135 characters cannot exceed m_codeLength.
136 */
137
138 /*!
139 \variable MsXpS::libXpertMassCore::PolChemDef::m_delimitedCodes
140
141 \brief The set of \l Monomer codes separated by '@' characters, like
142 "@Ala@Tyr@Phe@".
143 */
144
145 /*!
146 \variable MsXpS::libXpertMassCore::PolChemDef::m_ionizer
147
148 \brief The \l{Ionizer}{ionization agent} that governs the manner the \l
149 Polymer sequences of this polymer chemistry definition are ionized by default.
150 */
151
152 /*!
153 \variable MsXpS::libXpertMassCore::PolChemDef::msp_isotopicData
154
155 \brief The isotopic data defining the fundamentals of this \l PolChemDef
156 instance.
157 */
158
159 /*!
160 \variable MsXpS::libXpertMassCore::PolChemDef::m_monomers
161
162 \brief The container of \l{Monomer}s defined to be part of this \l PolChemDef
163 instance.
164 */
165
166
167 /*!
168 \variable MsXpS::libXpertMassCore::PolChemDef::m_modifs
169
170 \brief The container of \l{Modif}s defined to be part of this \l PolChemDef
171 instance.
172 */
173
174 /*!
175 \variable MsXpS::libXpertMassCore::PolChemDef::m_crossLinkers
176
177 The container of \l{CrossLinker}s defined to be part of this \l PolChemDef
178 instance.
179 */
180
181 /*!
182 \variable MsXpS::libXpertMassCore::PolChemDef::m_cleavageAgents
183
184 \brief The container of \l{CleavageAgent}s defining the various ways to cleave
185 \l Polymer sequences of this \l PolChemDef instance.
186 */
187
188 /*!
189 \variable MsXpS::libXpertMassCore::PolChemDef::m_fragmentationPathways
190
191 \brief The container of \l{FragmentationPathway}s defining the various ways to
192 fragment \l Oligomer sequences of this \l PolChemDef instance.
193 */
194
195 /*!
196 \variable MsXpS::libXpertMassCore::PolChemDef::m_polChemDefs
197
198 \brief The container of \l PolChemDef instances available in the repositories.
199 */
200
201
202 /*!
203 \variable MsXpS::libXpertMassCore::POL_CHEM_DEF_FILE_FORMAT_VERSION
204
205 \brief The latest version of the format of the file containing the
206 polymer chemistry definition.
207
208 Brought to 1 30 january 2023 for massXpert2
209 Brought to 2 10 november 2024 for massXpert2
210 */
211
212 const int POL_CHEM_DEF_FILE_FORMAT_VERSION = 2;
213
214 /*!
215 \brief Constructs a polymer chemistry definition.
216 */
217
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 77 PolChemDef::PolChemDef()
218 {
219 77 }
220
221 /*!
222 \brief Constructs a polymer chemistry definition on the basis of \a
223 pol_chem_def_spec.
224
225 The \a pol_chem_def_spec polymer chemistry definition specification provides
226 the name of the polymer chemistry definition and of the file that contains
227 it.
228 */
229
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 3 PolChemDef::PolChemDef(const PolChemDefSpec &pol_chem_def_spec)
230 {
231
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 3 m_name = pol_chem_def_spec.getName();
232
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 3 m_xmlDataFilePath = pol_chem_def_spec.getFilePath();
233
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 3 }
234
235 /*!
236 \brief Destroys the polymer chemistry definition
237 */
238 156 PolChemDef::~PolChemDef()
239 {
240
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 158 }
241
242 /*!
243 \brief Sets the \a name of this PolChemDef instance.
244 */
245 void
246 71 PolChemDef::setName(const QString &name)
247 {
248 71 m_name = name;
249 71 }
250
251 /*!
252 \brief Returns the name of this PolChemDef instance.
253 */
254 QString
255 4 PolChemDef::getName() const
256 {
257
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 4 return m_name;
258 }
259
260 /*!
261 \brief Sets the \a file_path of this PolChemDef instance.
262 */
263 void
264 72 PolChemDef::setXmlDataFilePath(const QString &file_path)
265 {
266 72 m_xmlDataFilePath = file_path;
267 72 }
268
269 /*!
270 \brief Returns the file path of this PolChemDef instance.
271 */
272 QString
273 3 PolChemDef::getXmlDataFilePath() const
274 {
275
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 3 return m_xmlDataFilePath;
276 }
277
278 /*!
279 \brief Returns the absolute directory path of this PolChemDef instance.
280 */
281 QString
282 1 PolChemDef::getXmlDataDirPath() const
283 {
284 // qDebug() << "The xml data file path:" << m_xmlDataFilePath;
285
286 1 QFileInfo fileInfo(m_xmlDataFilePath);
287
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 1 QDir dir(fileInfo.dir());
288
289 // qDebug() << "Returning the pol chem def data dir path:" <<
290
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 1 dir.absolutePath();
291
292
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 2 return dir.absolutePath();
293 1 }
294
295 /*!
296 \brief Sets the path of the isotopic data file to \a file_path.
297 */
298 void
299 68 PolChemDef::setIsotopicDataFilePath(const QString &file_path)
300 {
301 68 m_isotopicDataFilePath = file_path;
302 68 }
303
304 /*!
305 \brief Returns the path of the isotopic data file.
306 */
307 QString
308 69 PolChemDef::getIsotopicDataFilePath() const
309 {
310
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 69 return m_isotopicDataFilePath;
311 }
312
313 /*!
314 \brief Returns the path of the isotopic data file.
315
316 The deduction is based on the fact that the file should have
317 "isotopic-data.dat" as its name.
318 */
319 QString
320 70 PolChemDef::deduceIsotopicDataFilePath() const
321 {
322 // From the xml data file path, deduce the file name of the isotopic data.
323 70 QFileInfo file_info(m_xmlDataFilePath);
324
325
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 70 if(!file_info.exists())
326 ✗ qFatal(
327 "Programming error. The polymer chemistry definition file could not be "
328 "found.");
329
330
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 70 QDir dir(file_info.dir());
331
332
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 70 QString isotopic_data_file_path =
333
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 140 dir.absolutePath() + QDir::separator() + "isotopic-data.dat";
334
335 70 return isotopic_data_file_path;
336 70 }
337
338 /*!
339 \brief Sets the left cap \a formula.
340 */
341 void
342 ✗ PolChemDef::setLeftCap(const Formula &formula)
343 {
344 ✗ m_leftCap = formula;
345 ✗ }
346
347 /*!
348 \brief Returns the left cap formula.
349 */
350 const Formula &
351 1019 PolChemDef::getLeftCap() const
352 {
353 1019 return m_leftCap;
354 }
355
356 /*!
357 \brief Sets the right cap \a formula.
358 */
359 void
360 ✗ PolChemDef::setRightCap(const Formula &formula)
361 {
362 ✗ m_rightCap = formula;
363 ✗ }
364
365 /*!
366 \brief Returns the right cap formula.
367 */
368 const Formula &
369 987 PolChemDef::getRightCap() const
370 {
371 987 return m_rightCap;
372 }
373
374 /*!
375 \brief Sets the \a code_length.
376 */
377 void
378 ✗ PolChemDef::setCodeLength(int code_length)
379 {
380 ✗ m_codeLength = code_length;
381 ✗ }
382
383 /*!
384 \brief Returns the code length.
385 */
386 int
387 133226 PolChemDef::getCodeLength() const
388 {
389 133226 return m_codeLength;
390 }
391
392 /*!
393 \brief Sets the ionizer to \a ionizer.
394 */
395 void
396 ✗ PolChemDef::setIonizer(const Ionizer &ionizer)
397 {
398 ✗ m_ionizer = ionizer;
399 ✗ }
400
401 /*!
402 \brief Returns a const reference to the ionizer.
403 */
404 const Ionizer &
405 1 PolChemDef::getIonizerCstRef() const
406 {
407 1 return m_ionizer;
408 }
409
410 /*!
411 \brief Returns a pointer to the ionizer.
412 */
413 Ionizer &
414 ✗ PolChemDef::getIonizerRef()
415 {
416 ✗ return m_ionizer;
417 }
418
419 /*!
420 \brief Sets the isotopic data to \a isotopic_data_sp.
421 */
422 void
423 ✗ PolChemDef::setIsotopicDataSPtr(IsotopicDataSPtr isotopic_data_sp)
424 {
425 ✗ msp_isotopicData = isotopic_data_sp;
426 ✗ }
427
428 /*!
429 \brief Returns the isotopic data as const shared pointer..
430 */
431 IsotopicDataCstSPtr
432 422743 PolChemDef::getIsotopicDataCstSPtr() const
433 {
434 422743 return msp_isotopicData;
435 }
436
437 /*!
438 \brief Returns the isotopic data as non-const shared pointer..
439 */
440 IsotopicDataSPtr
441 136 PolChemDef::getIsotopicDataSPtr()
442 {
443 136 return msp_isotopicData;
444 }
445
446 //////////////////// MODIFS //////////////////////
447 //////////////////// MODIFS //////////////////////
448
449 /*!
450 \brief Returns a const reference to the list of modifications.
451 */
452 const std::vector<ModifSPtr> &
453 13 PolChemDef::getModifsCstRef() const
454 {
455 13 return m_modifs;
456 }
457
458 /*!
459 \brief Returns a pointer to the list of modifications.
460 */
461 std::vector<ModifSPtr> &
462 ✗ PolChemDef::getModifsRef()
463 {
464 ✗ return m_modifs;
465 }
466
467 /*!
468 \brief Returns a pointer to the Modif instance known under \a name.
469
470 If no Modif by that \a name is known, nullptr is returned.
471 */
472 ModifCstSPtr
473 396 PolChemDef::getModifCstSPtrByName(const QString &name) const
474 {
475
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 396 ModifsCstIterator the_iterator_cst = std::find_if(
476
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 3560 m_modifs.cbegin(), m_modifs.cend(), [name](const auto &modif_csp) {
477 5115 return modif_csp->getName() == name;
478 });
479
480
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 396 if(the_iterator_cst == m_modifs.cend())
481 4 return nullptr;
482
483 392 return (*the_iterator_cst);
484 }
485
486 /*!
487 \brief Returns the index of the \l Modif in the member container of
488 these instances or -1 if that was not found.
489
490 The search is performed using the \a name of the Modif.
491 */
492 int
493 ✗ PolChemDef::getModifIndexByName(const QString &name) const
494 {
495 ✗ ModifsCstIterator the_iterator_cst = std::find_if(
496 ✗ m_modifs.cbegin(), m_modifs.cend(), [name](const auto &modif_csp) {
497 ✗ bool same_name = (modif_csp->getName() == name);
498 ✗ return same_name;
499 });
500
501 ✗ if(the_iterator_cst == m_modifs.cend())
502 return -1;
503
504 ✗ return std::distance(m_modifs.cbegin(), the_iterator_cst);
505 }
506
507 //////////////////// MONOMERS //////////////////////
508 //////////////////// MONOMERS //////////////////////
509
510 /*!
511 \brief Returns a const reference to the list of modifications.
512 */
513 const std::vector<MonomerSPtr> &
514 13 PolChemDef::getMonomersCstRef() const
515 {
516 13 return m_monomers;
517 }
518
519 /*!
520 \brief Returns a pointer to the list of Monomer instances.
521 */
522 std::vector<MonomerSPtr> &
523 ✗ PolChemDef::getMonomersRef()
524 {
525 ✗ return m_monomers;
526 }
527
528 /*!
529 \brief Returns a pointer to the Monomer instance known under \a name.
530
531 If no Monomer by that \a name is known, nullptr is returned.
532 */
533 MonomerSPtr
534 10 PolChemDef::getMonomerCstSPtrByName(const QString &name) const
535 {
536
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 10 MonomersCstIterator the_iterator_cst = std::find_if(
537
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 86 m_monomers.cbegin(), m_monomers.cend(), [name](const auto &monomer_csp) {
538 204 return monomer_csp->getName() == name;
539 });
540
541
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 10 if(the_iterator_cst == m_monomers.cend())
542 4 return nullptr;
543
544 6 return (*the_iterator_cst);
545 }
546
547 /*!
548 \brief Returns a pointer to the Monomer instance known under \a code.
549
550 If no Monomer by that \a code is known, nullptr is returned.
551 */
552 MonomerSPtr
553 75381 PolChemDef::getMonomerCstSPtrByCode(const QString &code) const
554 {
555
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 75381 MonomersCstIterator the_iterator_cst = std::find_if(
556
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 678429 m_monomers.cbegin(), m_monomers.cend(), [code](const auto &monomer_csp) {
557 738413 return monomer_csp->getCode() == code;
558 });
559
560
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 75381 if(the_iterator_cst == m_monomers.cend())
561 15 return nullptr;
562
563 75366 return (*the_iterator_cst);
564 }
565
566 /*!
567 \brief Returns the index of the \l Monomer in the member container of
568 these instances or -1 if that was not found.
569
570 The search is performed using the \a name of the Monomer.
571 */
572 int
573 ✗ PolChemDef::getMonomerIndexByName(const QString &name) const
574 {
575 ✗ MonomersCstIterator the_iterator_cst = std::find_if(
576 ✗ m_monomers.cbegin(), m_monomers.cend(), [name](const auto &monomer_csp) {
577 ✗ bool same_name = (monomer_csp->getName() == name);
578 ✗ return same_name;
579 });
580
581 ✗ if(the_iterator_cst == m_monomers.cend())
582 return -1;
583
584 ✗ return std::distance(m_monomers.cbegin(), the_iterator_cst);
585 }
586
587 /*!
588 \brief Returns the index of the \l Monomer in the member container of
589 these instances or -1 if that was not found.
590
591 The search is performed using the \a code of the Monomer.
592 */
593 int
594 ✗ PolChemDef::getMonomerIndexByCode(const QString &code) const
595 {
596 ✗ MonomersCstIterator the_iterator_cst = std::find_if(
597 ✗ m_monomers.cbegin(), m_monomers.cend(), [code](const auto &monomer_csp) {
598 ✗ bool same_code = (monomer_csp->getCode() == code);
599 ✗ return same_code;
600 });
601
602 ✗ if(the_iterator_cst == m_monomers.cend())
603 return -1;
604
605 ✗ return std::distance(m_monomers.cbegin(), the_iterator_cst);
606 }
607
608 //////////////////// CROSSLINKERS //////////////////////
609 //////////////////// CROSSLINKERS //////////////////////
610
611 /*!
612 \brief Returns a const reference to the list of modifications.
613 */
614 const std::vector<CrossLinkerSPtr> &
615 4 PolChemDef::getCrossLinkersCstRef() const
616 {
617 4 return m_crossLinkers;
618 }
619
620 /*!
621 \brief Returns a pointer to the list of CrossLinker instances.
622 */
623 std::vector<CrossLinkerSPtr> &
624 ✗ PolChemDef::getCrossLinkersRef()
625 {
626 ✗ return m_crossLinkers;
627 }
628
629 /*!
630 \brief Returns a pointer to the CrossLinker instance known under \a name.
631
632 If no CrossLinker by that \a name is known, nullptr is returned.
633 */
634 CrossLinkerCstSPtr
635 69 PolChemDef::getCrossLinkerCstSPtrByName(const QString &name) const
636 {
637
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 69 CrossLinkersCstIterator the_iterator_cst =
638 138 std::find_if(m_crossLinkers.cbegin(),
639 m_crossLinkers.cend(),
640
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 621 [name](const auto &crossLinker_csp) {
641 121 bool same_name = (crossLinker_csp->getName() == name);
642 121 return same_name;
643 });
644
645
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 69 if(the_iterator_cst == m_crossLinkers.cend())
646 ✗ return nullptr;
647
648 69 return (*the_iterator_cst);
649 }
650
651 //////////////////// CLEAVAGE AGENTS //////////////////////
652 //////////////////// CLEAVAGE AGENTS //////////////////////
653
654 /*!
655 \brief Returns a const reference to the list of modifications.
656 */
657 const std::vector<CleavageAgentSPtr> &
658 1 PolChemDef::getCleavageAgentsCstRef() const
659 {
660 1 return m_cleavageAgents;
661 }
662
663 /*!
664 \brief Returns a pointer to the list of CleavageAgent instances.
665 */
666 std::vector<CleavageAgentSPtr> &
667 ✗ PolChemDef::getCleavageAgentsRef()
668 {
669 ✗ return m_cleavageAgents;
670 }
671
672 /*!
673 \brief Returns a pointer to the CleavageAgent instance known under \a name.
674
675 If no CleavageAgent by that \a name is known, nullptr is returned.
676 */
677 CleavageAgentCstSPtr
678 8 PolChemDef::getCleavageAgentCstSPtrByName(const QString &name) const
679 {
680
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 8 CleavageAgentsCstIterator the_iterator_cst =
681 16 std::find_if(m_cleavageAgents.cbegin(),
682 m_cleavageAgents.cend(),
683
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 68 [name](const auto &cleavage_agent_csp) {
684
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 12 bool same_name = (cleavage_agent_csp->getName() == name);
685 return same_name;
686 });
687
688
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 8 if(the_iterator_cst == m_cleavageAgents.cend())
689 1 return nullptr;
690
691 7 return (*the_iterator_cst);
692 }
693
694 /*!
695 \brief Returns the index of the \l CleavageAgent in the member container of
696 these instances or -1 if that was not found.
697
698 The search is performed using the \a name of the CleavageAgent.
699 */
700 int
701 ✗ PolChemDef::getCleavageAgentIndexByName(const QString &name) const
702 {
703 ✗ CleavageAgentsCstIterator the_iterator_cst =
704 ✗ std::find_if(m_cleavageAgents.cbegin(),
705 m_cleavageAgents.cend(),
706 ✗ [name](const auto &cleavage_agent_csp) {
707 ✗ bool same_name = (cleavage_agent_csp->getName() == name);
708 return same_name;
709 });
710
711 ✗ if(the_iterator_cst == m_cleavageAgents.cend())
712 return -1;
713
714 ✗ return std::distance(m_cleavageAgents.cbegin(), the_iterator_cst);
715 }
716
717 //////////////////// FRAGMENTATION PATHWAYS //////////////////////
718 //////////////////// FRAGMENTATION PATHWAYS //////////////////////
719
720 /*!
721 \brief Returns a const reference to the list of modifications.
722 */
723 const std::vector<FragmentationPathwaySPtr> &
724 1 PolChemDef::getFragmentationPathwaysCstRef() const
725 {
726 1 return m_fragmentationPathways;
727 }
728
729 /*!
730 \brief Returns a pointer to the list of FragmentationPathway instances.
731 */
732 std::vector<FragmentationPathwaySPtr> &
733 ✗ PolChemDef::getFragmentationPathwaysRef()
734 {
735 ✗ return m_fragmentationPathways;
736 }
737
738 /*!
739 \brief Returns a pointer to the FragmentationPathway instance known under \a
740 name.
741
742 If no FragmentationPathway by that \a name is known, nullptr is returned.
743 */
744 FragmentationPathwayCstSPtr
745 4 PolChemDef::getFragmentationPathwayCstSPtrByName(const QString &name) const
746 {
747
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 4 FragmentationPathwaysCstIterator the_iterator_cst =
748 8 std::find_if(m_fragmentationPathways.cbegin(),
749 m_fragmentationPathways.cend(),
750
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 36 [name](const auto &fragmentation_pathway_csp) {
751 bool same_name =
752
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 7 (fragmentation_pathway_csp->getName() == name);
753 return same_name;
754 });
755
756
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 4 if(the_iterator_cst == m_fragmentationPathways.cend())
757 ✗ return nullptr;
758
759 4 return (*the_iterator_cst);
760 }
761
762 /*!
763 \brief Returns the index of the \l FragmentationPathway in the member container
764 of these instances or -1 if that was not found.
765
766 The search is performed using the \a name of the FragmentationPathway.
767 */
768 int
769 ✗ PolChemDef::getFragmentationPathwayIndexByName(const QString &name) const
770 {
771 ✗ FragmentationPathwaysCstIterator the_iterator_cst =
772 ✗ std::find_if(m_fragmentationPathways.cbegin(),
773 m_fragmentationPathways.cend(),
774 ✗ [name](const auto &cleavage_agent_csp) {
775 ✗ bool same_name = (cleavage_agent_csp->getName() == name);
776 return same_name;
777 });
778
779 ✗ if(the_iterator_cst == m_fragmentationPathways.cend())
780 return -1;
781
782 ✗ return std::distance(m_fragmentationPathways.cbegin(), the_iterator_cst);
783 }
784
785 /*!
786 \brief Constructs a string with the codes of all the \l{Monomer}s in this
787 PolChemDef instance.
788
789 The codes are delimited by the '@' character.
790
791 Returns true.
792 */
793 bool
794 ✗ PolChemDef::calculateDelimitedCodes()
795 {
796 // We have to produce a QString containing all the codes from the
797 // monomers known to this polymer chemistry definition.
798
799 ✗ m_delimitedCodes.clear();
800 ✗ m_delimitedCodes.append('@');
801
802 ✗ for(auto monomer_csp : m_monomers)
803 {
804
805 ✗ m_delimitedCodes.append(monomer_csp->getCode());
806 ✗ m_delimitedCodes.append('@');
807 ✗ }
808
809 // Close the string with a delim char:
810 ✗ m_delimitedCodes.append('@');
811
812 ✗ return true;
813 }
814
815 /*!
816 \brief Returns a string with the codes of all the \l{Monomer}s in this
817 PolChemDef instance.
818
819 The codes are delimited by the '@' character.
820 */
821 const QString &
822 ✗ PolChemDef::getDelimitedCodes()
823 {
824 ✗ if(m_delimitedCodes.isEmpty())
825 ✗ calculateDelimitedCodes();
826
827 ✗ return m_delimitedCodes;
828 }
829
830 /*!
831 \brief Returns a string list with the mass difference between all the
832 \l{Monomer}s in this PolChemDef instace.
833
834 If the difference is below the \a threshold, the difference is added to
835 the string list, otherwise it is skipped. The masses that are compared
836 between every two monomers is of \a mass_type.
837 */
838 QStringList
839 ✗ PolChemDef::differenceBetweenMonomers(double threshold,
840 Enums::MassType mass_type)
841 {
842 // qDebug()
843 // << "threshold" << threshold;
844
845 ✗ QStringList difference_list;
846
847 ✗ if(mass_type != Enums::MassType::MONO && mass_type != Enums::MassType::AVG)
848 {
849 qDebug() << "Please set the mass type "
850 "to either Enums::MassType::MONO or "
851 "Enums::MassType::AVG";
852 return difference_list;
853 }
854
855 // We iterate in the list of monomers and compute a difference of
856 // mass for each monomer with respect to all the other ones. If
857 // the mass difference is less or equal to the threshold, then the
858 // pair is returned.
859
860 ✗ if(m_monomers.size() < 2)
861 return difference_list;
862
863 MonomersCstIterator iterator_outer_loop_cst = m_monomers.cbegin();
864
865 ✗ while(iterator_outer_loop_cst != m_monomers.cend())
866 {
867 ✗ Monomer outer_monomer = *(*iterator_outer_loop_cst);
868
869 ✗ outer_monomer.calculateMasses(/*IsotopicDataCstSPtr*/ nullptr);
870
871 ✗ MonomersCstIterator iterator_inner_loop_cst = m_monomers.cbegin();
872
873 ✗ while(iterator_inner_loop_cst != m_monomers.cend())
874 {
875 ✗ if(*iterator_outer_loop_cst == *iterator_inner_loop_cst)
876 {
877 ✗ ++iterator_inner_loop_cst;
878 ✗ continue;
879 }
880
881 ✗ Monomer inner_monomer = *(*iterator_inner_loop_cst);
882
883 ✗ inner_monomer.calculateMasses(/*IsotopicDataCstSPtr*/ nullptr);
884
885 // At this point we have the masses for both monomers.
886
887 ✗ double mass_diff = 0;
888
889 ✗ if(mass_type == Enums::MassType::MONO)
890 {
891 ✗ mass_diff = outer_monomer.getMass(Enums::MassType::MONO) -
892 ✗ inner_monomer.getMass(Enums::MassType::MONO);
893 }
894 else
895 //(monoOrAvg == Enums::MassType::AVG)
896 {
897 ✗ mass_diff = outer_monomer.getMass(Enums::MassType::AVG) -
898 ✗ inner_monomer.getMass(Enums::MassType::AVG);
899 }
900
901 // At this point, make sure that diff is within the
902 // threshold. Note that to avoid duplicates, we remove all
903 // values that are negative.
904
905 ✗ if(mass_diff >= 0 && mass_diff <= threshold)
906 {
907 ✗ QString line = QString("%1 - %2 = %3")
908 ✗ .arg(outer_monomer.getName())
909 ✗ .arg(inner_monomer.getName())
910 ✗ .arg(mass_diff);
911
912 ✗ difference_list.append(line);
913 ✗ }
914 ✗ ++iterator_inner_loop_cst;
915 ✗ }
916 ✗ ++iterator_outer_loop_cst;
917 ✗ }
918
919 return difference_list;
920 ✗ }
921
922 //////////////// OPERATORS /////////////////////
923
924
925 /*!
926 \brief Returns true if this PolChemDef is equal to \a other, false otherwise.
927
928 The comparison is deep, with all the various chemical entities in the
929 various containers being compared (not their pointers, but the objects
930 themselves).
931
932 \note The names and the data file paths are not compared, because this
933 comparison operator is aimed at comparing the chemistries of the PolChemDef.
934 */
935 bool
936 1 PolChemDef::isChemicallyEquivalent(const PolChemDef &other) const
937 {
938
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939 return true;
940
941 1 if(m_name != other.m_name)
942 {
943 1 qDebug() << "The names are not identical.";
944 }
945
946
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 1 if(m_leftCap != other.m_leftCap)
947 {
948 qDebug() << "The left caps are not identical.";
949 return false;
950 }
951
952
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 1 if(m_rightCap != other.m_rightCap)
953 {
954 qDebug() << "The right caps are not identical.";
955 return false;
956 }
957
958
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 1 if(m_codeLength != other.m_codeLength)
959 {
960 qDebug() << "The code lengths are not identical.";
961 return false;
962 }
963
964
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 1 if(m_delimitedCodes != other.m_delimitedCodes)
965 {
966 qDebug() << "The delimited codes are not identical.";
967 return false;
968 }
969
970
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 1 if(m_ionizer != other.m_ionizer)
971 {
972 qDebug() << "The ionizers are not identical.";
973 return false;
974 }
975
976
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 1 if(msp_isotopicData != nullptr && other.msp_isotopicData != nullptr)
977 {
978 1 qDebug() << "Now checking the isotopic data";
979
980
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 1 if(*msp_isotopicData.get() != *other.msp_isotopicData.get())
981 {
982 qDebug() << "The isotopic data are not identical.";
983 return false;
984 }
985 }
986
987
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 1 if(m_modifs.size() != other.m_modifs.size())
988 {
989 qDebug() << "The modifs containers have not the same sizes.";
990 return false;
991 }
992
993 ModifsCstIterator this_modif_iterator_cst = m_modifs.cbegin();
994 ModifsCstIterator other_modif_iterator_cst = other.m_modifs.cbegin();
995
996
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997
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998 {
999
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 26 const Modif this_modif = *(*this_modif_iterator_cst);
1000
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 26 const Modif other_modif = *(*other_modif_iterator_cst);
1001
1002
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 26 if(this_modif != other_modif)
1003 {
1004 ✗ qDebug() << "At least one modification is not identical in both "
1005 "PolChemDef entities.";
1006 ✗ return false;
1007 }
1008
1009 26 ++this_modif_iterator_cst;
1010 26 ++other_modif_iterator_cst;
1011 26 }
1012
1013 // qDebug() << "The Modif instances are identical.";
1014
1015
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 1 if(m_monomers.size() != other.m_monomers.size())
1016 {
1017 qDebug() << "The monomers containers have not the same sizes.";
1018 return false;
1019 }
1020
1021 MonomersCstIterator this_monomer_iterator_cst = m_monomers.cbegin();
1022 MonomersCstIterator other_monomer_iterator_cst = other.m_monomers.cbegin();
1023
1024
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1025
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1026 {
1027
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1028
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 21 const Monomer other_monomer = *(*other_monomer_iterator_cst);
1029
1030
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 21 if(this_monomer != other_monomer)
1031 {
1032 ✗ qDebug()
1033 << "At least one monomer is not identical in both PolChemDef "
1034 "entities.";
1035 ✗ return false;
1036 }
1037
1038 21 ++this_monomer_iterator_cst;
1039 21 ++other_monomer_iterator_cst;
1040 21 }
1041
1042 // qDebug() << "The Monomer instances are identical.";
1043
1044
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 1 if(m_crossLinkers.size() != other.m_crossLinkers.size())
1045 {
1046 qDebug() << "The cross-linkers containers have not the same sizes.";
1047 return false;
1048 }
1049
1050 CrossLinkersCstIterator this_cross_linker_iterator_cst =
1051 m_crossLinkers.cbegin();
1052 CrossLinkersCstIterator other_cross_linker_iterator_cst =
1053 other.m_crossLinkers.cbegin();
1054
1055
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1056
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1057 {
1058
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1059 2 const CrossLinker other_cross_linker =
1060
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1061
1062
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 2 if(this_cross_linker != other_cross_linker)
1063 {
1064 ✗ qDebug().noquote()
1065 << "At least one cross-linker is not identical in both "
1066 "PolChemDef entities: \n"
1067 << this_cross_linker.toString() << "\nvs\n"
1068 << other_cross_linker.toString();
1069 ✗ return false;
1070 }
1071
1072 2 ++this_cross_linker_iterator_cst;
1073 2 ++other_cross_linker_iterator_cst;
1074 2 }
1075
1076 // qDebug() << "The CrossLinker instances are identical.";
1077
1078
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 1 if(m_cleavageAgents.size() != other.m_cleavageAgents.size())
1079 {
1080 qDebug()
1081 << "The cleavage specifications containers have not the same sizes.";
1082 return false;
1083 }
1084
1085 CleavageAgentsCstIterator this_cleavage_agent_iterator_cst =
1086 m_cleavageAgents.cbegin();
1087 CleavageAgentsCstIterator other_cleavage_agent_iterator_cst =
1088 other.m_cleavageAgents.cbegin();
1089
1090
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1091
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1092 {
1093
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 8 CleavageAgent this_cleavage_agent;
1094
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1095
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1097
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1098
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 8 if(this_cleavage_agent != other_cleavage_agent)
1100 {
1101 ✗ qDebug().noquote()
1102 << "At least one cleavage specification is not identical in "
1103 "both PolChemDef entities:\n"
1104 << this_cleavage_agent.toString() << "\nvs\n"
1105 << other_cleavage_agent.toString();
1106 ✗ return false;
1107 }
1108
1109 8 ++this_cleavage_agent_iterator_cst;
1110 8 ++other_cleavage_agent_iterator_cst;
1111 8 }
1112
1113 // qDebug() << "The CleavageAgent instances are identical.";
1114
1115
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 1 if(m_fragmentationPathways.size() != other.m_fragmentationPathways.size())
1116 {
1117 qDebug() << "The fragmentation specifications containers have not the "
1118 "same sizes.";
1119 return false;
1120 }
1121
1122 FragmentationPathwaysCstIterator this_fragmentation_pathway_iterator_cst =
1123 m_fragmentationPathways.cbegin();
1124 FragmentationPathwaysCstIterator other_fragmentation_pathway_iterator_cst =
1125 other.m_fragmentationPathways.cbegin();
1126
1127
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1128
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1129
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1130
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1131 {
1132 7 const FragmentationPathway this_fragmentation_pathway =
1133
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1134 7 const FragmentationPathway other_fragmentation_pathway =
1135
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1136
1137
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 7 if(this_fragmentation_pathway != other_fragmentation_pathway)
1138 {
1139 ✗ qDebug() << "At least one fragmentation specification is not "
1140 "identical in both PolChemDef entities.";
1141 ✗ return false;
1142 }
1143
1144 7 ++this_fragmentation_pathway_iterator_cst;
1145 7 ++other_fragmentation_pathway_iterator_cst;
1146 7 }
1147
1148 // qDebug() << "The FragmentationPathway instances are identical.";
1149
1150 return true;
1151 }
1152
1153 /*!
1154 \brief Returns true if this PolChemDef is equal to \a other, false otherwise.
1155
1156 The comparison is deep, with all the various chemical entities in the
1157 various containers being compared (not their pointers, but the objects
1158 themselves).
1159
1160 \note The names and the data file paths are not compared, because this
1161 comparison operator is aimed at comparing the chemistries of the PolChemDef.
1162 */
1163 bool
1164 ✗ PolChemDef::operator==(const PolChemDef &other) const
1165 {
1166 ✗ if(&other == this)
1167 return true;
1168
1169 ✗ if(!isChemicallyEquivalent(other))
1170 {
1171 qDebug() << "The PolChemDef are not chemically identical.";
1172 return false;
1173 }
1174
1175 if(m_name != other.m_name)
1176 {
1177 qDebug() << "The names are not identical.";
1178 }
1179
1180 if(m_xmlDataFilePath != other.m_xmlDataFilePath)
1181 {
1182 qDebug() << "The definition file paths are not identical.";
1183 }
1184
1185 if(m_isotopicDataFilePath != other.m_isotopicDataFilePath)
1186 {
1187 qDebug() << "The isotopic data file paths are not identical.";
1188 }
1189
1190 return true;
1191 }
1192
1193 /*!
1194 \brief Returns true if \c this and \a other differ.
1195
1196 Returns the negated result of operator==().
1197 */
1198 bool
1199 ✗ PolChemDef::operator!=(const PolChemDef &other) const
1200 {
1201 ✗ if(&other == this)
1202 return false;
1203
1204 ✗ return !operator==(other);
1205 }
1206
1207 /*!
1208 \brief Loads the isotopic data stored in the file \a file_path.
1209
1210 The data loaded from file are parsed and validated. Upon parsing of the
1211 file, the data are stored in the \a pol_chem_def_sp instance's isotopic
1212 data member.
1213
1214 If \a file_path is empty, it is reconstructed using the directory of the
1215 polymer chemistry definition and the fact that the isotopic data file name
1216 is "isotopic-data.dat".
1217
1218 Returns the count of parsed isotopes.
1219 */
1220 std::size_t
1221 69 PolChemDef::loadIsotopicData(PolChemDefSPtr pol_chem_def_sp,
1222 const QString &file_path)
1223 {
1224 // There are three situations:
1225 //
1226 // 1. The file_path exists and the data are loaded from there.
1227 //
1228 // 2. A file named isotopic-data.dat is found in the polymer chemistry
1229 // definition directory and it is loaded.
1230 //
1231 // 3. No file named isotopic-data.dat is found in the polymer chemistry
1232 // defintion directory and then data are loaded from the IsoSpec tables.
1233
1234 // If the provided argument is not empty and actually describes an
1235 // existing file, then save the data there.
1236
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 69 QString local_file_path(file_path);
1237
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 69 QFileInfo local_file_info(local_file_path);
1238
1239
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 69 if(local_file_path.isEmpty() || !local_file_info.exists())
1240 {
1241 // qDebug() << "The provided file name" << file_path << "does not
1242 // exist.";
1243
1244 // Then try the member datum that provides the name of the file from
1245 // which to load the isotopic data.
1246
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 69 local_file_path = pol_chem_def_sp->getIsotopicDataFilePath();
1247
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 69 local_file_info.setFile(local_file_path);
1248
1249
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 69 if(local_file_path.isEmpty() || !local_file_info.exists())
1250 {
1251 // qDebug() << "The member datum file name " << local_file_path
1252 //<< "does not exist.";
1253
1254 // Last resort: deduce the isotopic data file name from the
1255 // directory of the polymer chemistry definition.
1256
1257
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 69 local_file_path = pol_chem_def_sp->deduceIsotopicDataFilePath();
1258
1259 // qDebug() << "Crafted the isotopic-data.dat file path:"
1260 //<< local_file_path;
1261
1262 // Finally for a later last check:
1263
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 69 local_file_info.setFile(local_file_path);
1264 }
1265 }
1266
1267 // qDebug() << "Allocating brand new isotopic data instance.";
1268
1269 // At this point we can delete the pre-exsting isotopic data.
1270
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 69 pol_chem_def_sp->msp_isotopicData = std::make_shared<IsotopicData>();
1271
1272 // Allocate a specific handler to the kind of isotopic data (library
1273 // tables or user file).
1274
1275 69 std::size_t count = 0;
1276
1277
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 69 if(local_file_path.isEmpty() || !local_file_info.exists())
1278 {
1279 // qDebug() << "Loading the isotopic data from the library.";
1280
1281 1 IsotopicDataLibraryHandler isotopic_data_handler(
1282
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 1 pol_chem_def_sp->msp_isotopicData);
1283
1284 1 qsizetype non_isotope_skipped_items = 0;
1285
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 1 count = isotopic_data_handler.loadData(non_isotope_skipped_items);
1286 1 }
1287 else
1288 {
1289 // qDebug() << "Loading the isotopic data from file:" << local_file_path;
1290
1291 68 IsotopicDataUserConfigHandler isotopic_data_handler(
1292
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 136 pol_chem_def_sp->msp_isotopicData);
1293
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 68 count = isotopic_data_handler.loadData(local_file_path);
1295
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 68 if(!count)
1297 {
1298 ✗ qDebug() << "Failed to load any isotopic data.";
1299 ✗ return false;
1300 }
1301
1302 // Now set the file path to the pol chem def.
1303
1304
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 68 pol_chem_def_sp->setIsotopicDataFilePath(local_file_path);
1305 68 }
1306
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 69 if(!count)
1308 {
1309 qDebug() << "Failed to load any isotopic data.";
1310 return false;
1311 }
1312
1313 return count;
1314 69 }
1315
1316 /*!
1317 \brief Writes the isotopic data in the \a pol_chem_def_sp PolChemDef
1318 instance to file \a file_path.
1319
1320 Returns the count of isotopes written to file.
1321 */
1322 std::size_t
1323 ✗ PolChemDef::writeIsotopicData(PolChemDefSPtr pol_chem_def_sp,
1324 const QString &file_path)
1325 {
1326 // There are three situations:
1327 //
1328 // 1. The file_path is not empty and the data are saved there.
1329 //
1330 // 2. The file_path is empty and the data are stored in the member file
1331 // path name (if not empty).
1332 //
1333 // 3. The file path is crafted from the directory of the polymer
1334 // chemistry definition.
1335
1336
1337 // Whatever the situation, the isotopic data handler we need here is
1338 // this one:
1339 ✗ IsotopicDataUserConfigHandler isotopic_data_handler(
1340 ✗ pol_chem_def_sp->msp_isotopicData);
1341
1342 // We'll instantiate the proper isotopic data handler depending on the
1343 // situation.
1344
1345 ✗ if(!file_path.isEmpty())
1346 {
1347 // We have a file name, store in there.
1348 ✗ pol_chem_def_sp->setIsotopicDataFilePath(file_path);
1349 ✗ return isotopic_data_handler.writeData(file_path);
1350 }
1351
1352 // Check the member datum.
1353
1354 ✗ if(!pol_chem_def_sp->m_isotopicDataFilePath.isEmpty())
1355 {
1356 // We have a file name, store in there.
1357 ✗ return isotopic_data_handler.writeData(
1358 ✗ pol_chem_def_sp->m_isotopicDataFilePath);
1359 }
1360
1361 // Last resort: deduce the isotopic data file name from the directory
1362 // of the polymer chemistry definition.
1363
1364 ✗ QString local_file_path = pol_chem_def_sp->getXmlDataDirPath();
1365 ✗ QFileInfo local_file_info(local_file_path);
1366
1367 ✗ if(!local_file_info.exists())
1368 ✗ qFatal(
1369 "Programming error. At this stage the name of the polymer "
1370 "chemistry definition file should be known.");
1371
1372 ✗ QDir dir(local_file_info.dir());
1373
1374 ✗ local_file_path =
1375 ✗ dir.absolutePath() + QDir::separator() + "isotopic-data.dat";
1376
1377 ✗ pol_chem_def_sp->setIsotopicDataFilePath(local_file_path);
1378
1379 ✗ return isotopic_data_handler.writeData(local_file_path);
1380 ✗ }
1381
1382 /*!
1383 \brief Parses the polymer chemistry definition file and updates \a
1384 pol_chem_def_sp accordingly.
1385
1386 Upon parsing of the file and validation of the data, the \a
1387 pol_chem_def_sp is updated, essentially initializing it with the data from
1388 the file.
1389
1390 Note that the \a pol_chem_def_sp should have a working set of isotopic
1391 data.
1392
1393 Returns true if the parsing was successful and false otherwise.
1394 */
1395 bool
1396 67 PolChemDef::renderXmlPolChemDefFileVersion1(PolChemDefSPtr pol_chem_def_sp)
1397 {
1398 67 qDebug() << "Rendering PolChemDef file VERSION 1.";
1399
1400
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 67 if(pol_chem_def_sp == nullptr && pol_chem_def_sp.get() == nullptr)
1401 ✗ qFatalStream()
1402 ✗ << "Programming error. The PolChemDef pointer cannot be nullptr.";
1403
1404 // qDebug() << "The PolChemDef *:" << pol_chem_def_sp.get()
1405 //<< "and usage:" << pol_chem_def_sp.use_count();
1406
1407 ///////////////////// ATTENTION ///////////////////
1408 // Before reading the polymer chemistry data file, we need to make sure
1409 // we actually have read the isotopic data!
1410
1411 // qDebug() << "First check if we have isotopic data ready.";
1412
1413
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 134 if(pol_chem_def_sp->getIsotopicDataSPtr() == nullptr)
1414 {
1415 // qDebug() << "No isotopic data found in the polymer chemistry "
1416 // "definition, need to load the data.";
1417
1418 // First read the data!
1419 ✗ std::size_t count = pol_chem_def_sp->loadIsotopicData(pol_chem_def_sp);
1420
1421 ✗ if(!count)
1422 ✗ qFatal("Programming error. The isotopic data could not be loaded.");
1423
1424 // qDebug() << "At this point the isotopic data were loaded fine
1425 // with"
1426 //<< count << "isotopes loaded.";
1427 }
1428
1429
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 67 QDomDocument doc("polChemDefData");
1430
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 67 QDomElement element;
1431
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 67 QDomElement child;
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 67 QDomElement indentedChild;
1433
1434
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 67 QFile file(pol_chem_def_sp->m_xmlDataFilePath);
1435
1436 // qDebug() << "The polymer chemistry definition file:"
1437 // << pol_chem_def_sp->m_xmlDataFilePath;
1438
1439 // The general structure of the file we are reading is this:
1440 //
1441 // <polchemdefinition version="1">
1442 // <polchemdefdata">
1443 // <name>protein</name>
1444 // <leftcap>+H</leftcap>
1445 // <rightcap>+OH</rightcap>
1446 // <codelen>1</codelen>
1447 // <ionizerule>
1448 // <formula>+H</formula>
1449 // <charge>1</charge>
1450 // <level>1</level>
1451 // </ionizerule>
1452 // <monomers>
1453 // <mnm>
1454 // <name>Glycine</name>
1455 // <code>G</code>
1456 // <formula>C2H3NO</formula>
1457 // </mnm>
1458 // </monomers>
1459 // <modifs>
1460 // <mdf>
1461 // <name>Phosphorylation</name>
1462 // <formula>-H+H2PO3</formula>
1463 // </mdf>
1464 // </modifs>
1465 // <cleavespecs>
1466 // <cls>
1467 // <name>CyanogenBromide</name>
1468 // <pattern>M/</pattern>
1469 // <clr>
1470 // <re-mnm-code>M</re-mnm-code>
1471 // <re-formula>-CH2S+O</re-formula>
1472 // </clr>
1473 // </cls>
1474 // </cleavespecs>
1475 // <fragspecs>
1476 // <fgs>
1477 // <name>a</name>
1478 // <end>LE</end>
1479 // <formula>-C1O1</formula>
1480 // <fgr>
1481 // <name>a-fgr-1</name>
1482 // <formula>+H200</formula>
1483 // <prev-mnm-code>E</prev-mnm-code>
1484 // <this-mnm-code>D</this-mnm-code>
1485 // <next-mnm-code>F</next-mnm-code>
1486 // <comment>comment here!</comment>
1487 // </fgr>
1488 // </fgs>
1489 // </fragspecs>
1490 // </polchemdefdata>
1491 // </polchemdefinition>
1492
1493
1494
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 67 if(!file.open(QIODevice::ReadOnly))
1495 return false;
1496
1497
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 67 if(!doc.setContent(&file))
1498 {
1499 ✗ qDebug() << "Failed to set doc content.";
1500
1501 ✗ file.close();
1502 return false;
1503 }
1504
1505
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 67 file.close();
1506
1507 // qDebug() << "Closed the polymer chemistry definition file.";
1508
1509
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 67 element = doc.documentElement();
1510
1511
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 134 if(element.tagName() != "polchemdefinition")
1512 {
1513 qDebug() << "Polymer chemistry definition file is erroneous\n";
1514 return false;
1515 }
1516
1517 ///////////////////////////////////////////////
1518 // Check the version of the document.
1519
1520 67 QString text;
1521
1522
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 67 if(!element.hasAttribute("version"))
1523 ✗ text = "1";
1524 else
1525
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 67 text = element.attribute("version");
1526
1527 67 qDebug() << "The format of the definition:" << text;
1528
1529 67 bool ok = false;
1530
1531
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 67 int version = text.toInt(&ok, 10);
1532
1533
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 67 if(version != 1 || !ok)
1534 {
1535 qDebug() << "Polymer chemistry definition file has bad "
1536 "version number:"
1537 << version;
1538
1539 return false;
1540 }
1541
1542 //////////////////////////////////////////////
1543 // <polymer chemistry data>
1544
1545
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 134 child = element.firstChildElement();
1546
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 134 if(child.tagName() != "polchemdefdata")
1547 {
1548 qDebug() << "Polymer chemistry definition file is erroneous\n";
1549 return false;
1550 }
1551
1552 // <name>
1553
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1554
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 134 if(child.tagName() != "name")
1555 return false;
1556
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 67 pol_chem_def_sp->m_name = child.text();
1557
1558 // <leftcap>
1559
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 134 child = child.nextSiblingElement();
1560
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 134 if(child.tagName() != "leftcap")
1561 return false;
1562
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 67 pol_chem_def_sp->m_leftCap.setActionFormula(child.text());
1563
1564 // <rightcap>
1565
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 134 child = child.nextSiblingElement();
1566
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 134 if(child.tagName() != "rightcap")
1567 return false;
1568
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 67 pol_chem_def_sp->m_rightCap.setActionFormula(child.text());
1569
1570 // <codelen>
1571
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 134 child = child.nextSiblingElement();
1572
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 134 if(child.tagName() != "codelen")
1573 return false;
1574 67 ok = false;
1575
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 134 pol_chem_def_sp->m_codeLength = child.text().toInt(&ok);
1576
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 67 if(pol_chem_def_sp->m_codeLength == 0 && !ok)
1577 return false;
1578 67 qDebug() << "Now set the code length to" << pol_chem_def_sp->m_codeLength;
1579
1580 // <ionizerule>
1581
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 134 child = child.nextSiblingElement();
1582
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 134 if(child.tagName() != "ionizerule")
1583 return false;
1584
1585 // It is essential that we endow the Ionizer with the IsotopicData !
1586
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 67 pol_chem_def_sp->m_ionizer.setIsotopicDataCstSPtr(
1587
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 67 pol_chem_def_sp->getIsotopicDataCstSPtr());
1588
1589 // Now we can render the Ionizer by looking into the <ionizerule> XML
1590 // element.
1591
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 67 if(!pol_chem_def_sp->m_ionizer.renderXmlIonizeRuleElement(child))
1592 return false;
1593
1594 // Finally, we have to ascertain that the Ionizer is valid.
1595 67 ErrorList error_list;
1596
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 67 if(!pol_chem_def_sp->m_ionizer.validate(&error_list))
1597 {
1598 ✗ qCritical() << "The Ionizer is invalid, with errors:"
1599 ✗ << Utils::joinErrorList(error_list, ", ");
1600 ✗ return false;
1601 }
1602
1603 67 qDebug() << "Now starting the rendering of the <monomers> element.";
1604
1605 // <monomers>
1606
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 134 child = child.nextSiblingElement();
1607
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 134 if(child.tagName() != "monomers")
1608 return false;
1609
1610
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 134 indentedChild = child.firstChildElement();
1611
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 1474 while(!indentedChild.isNull())
1612 {
1613 1407 qDebug() << "Now rendering one of all the mnm elements.";
1614
1615
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 2814 if(indentedChild.tagName() != "mnm")
1616 {
1617 ✗ qCritical() << "The expected <mnm> element was not found.";
1618 ✗ return false;
1619 }
1620
1621 // Constructing a Monomer using the XML element ensures
1622 // that the masses are properly calculated for it, so
1623 // that MonomerCstSPtr point to fully qualified Monomer
1624 // instances that properly play the role of reference
1625 // throughout the chemical entities that involve Monomer
1626 // instances in the context of this PolChemDef.
1627
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 1407 MonomerSPtr monomer_sp =
1628 1407 std::make_shared<Monomer>(pol_chem_def_sp, indentedChild, version);
1629
1630
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 1407 if(!monomer_sp->isValid())
1631 {
1632 ✗ qDebug() << "Failed to render mnm element.";
1633
1634 ✗ monomer_sp.reset();
1635 ✗ return false;
1636 }
1637
1638
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 1407 pol_chem_def_sp->m_monomers.push_back(monomer_sp);
1639
1640
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 2814 indentedChild = indentedChild.nextSiblingElement();
1641 1407 }
1642
1643 67 qDebug() << "Size of MonomerList:"
1644 << pol_chem_def_sp->getMonomersCstRef().size()
1645 << "pol chem def usage:" << pol_chem_def_sp.use_count();
1646
1647 67 qDebug() << "Now starting the rendering of the <modifs> element.";
1648
1649 // <modifs>
1650
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1651
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 134 if(child.tagName() != "modifs")
1652 return false;
1653
1654
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 134 indentedChild = child.firstChildElement();
1655
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 1809 while(!indentedChild.isNull())
1656 {
1657
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 3484 if(indentedChild.tagName() != "mdf")
1658 ✗ return false;
1659
1660
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 1742 ModifSPtr modif_sp =
1661 1742 std::make_shared<Modif>(pol_chem_def_sp, indentedChild, version);
1662
1663
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 1742 if(!modif_sp->isValid())
1664 {
1665 ✗ qCritical()
1666 ✗ << "Failed to render the Modif instance from an XML <mdf> element.";
1667 ✗ modif_sp.reset();
1668 ✗ return false;
1669 }
1670
1671
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 1742 pol_chem_def_sp->m_modifs.push_back(modif_sp);
1672
1673
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 3484 indentedChild = indentedChild.nextSiblingElement();
1674 1742 }
1675
1676 67 qDebug() << "Size of ModifList:" << pol_chem_def_sp->getModifsCstRef().size()
1677 << "pol chem def usage:" << pol_chem_def_sp.use_count();
1678
1679 67 qDebug() << "Now starting the rendering of the <crosslinkers> element.";
1680
1681 // <crosslinkers>
1682 // Note that crosslinkers have appeared since version 3.
1683
1684
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 134 child = child.nextSiblingElement();
1685
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 134 if(child.tagName() != "crosslinkers")
1686 return false;
1687
1688
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 134 indentedChild = child.firstChildElement();
1689
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 201 while(!indentedChild.isNull())
1690 {
1691
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 268 if(indentedChild.tagName() != "clk")
1692 ✗ return false;
1693
1694
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 134 CrossLinkerSPtr crossLinker_sp =
1695 134 std::make_shared<CrossLinker>(pol_chem_def_sp, indentedChild, version);
1696
1697
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 134 if(!crossLinker_sp->isValid())
1698 {
1699 ✗ qCritical() << "Failed to render the CrossLinker instance from an "
1700 ✗ "XML <clk> element.";
1701 ✗ crossLinker_sp.reset();
1702 ✗ return false;
1703 }
1704
1705
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 134 pol_chem_def_sp->m_crossLinkers.push_back(crossLinker_sp);
1706
1707 134 qDebug() << "Rendered CrossLinker: " << crossLinker_sp->getName()
1708 << "with formula:" << crossLinker_sp->getFormula()
1709 << "with masses:"
1710 << crossLinker_sp->getMass(Enums::MassType::MONO) << "/"
1711 << crossLinker_sp->getMass(Enums::MassType::AVG);
1712
1713
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 268 indentedChild = indentedChild.nextSiblingElement();
1714 134 }
1715
1716 67 qDebug() << "Size of CrossLinker container:"
1717 << pol_chem_def_sp->getCrossLinkersCstRef().size()
1718 << "pol chem def usage:" << pol_chem_def_sp.use_count();
1719
1720 67 qDebug() << "Now starting the rendering of the <cleavespecs> element.";
1721
1722 // <cleavespecs>
1723
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1724
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 134 if(child.tagName() != "cleavespecs")
1725 {
1726 ✗ qCritical() << "Failed to load PolChemDef file: <cleavespecs> element "
1727 ✗ "not found.";
1728 ✗ return false;
1729 }
1730
1731
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 134 indentedChild = child.firstChildElement();
1732
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 603 while(!indentedChild.isNull())
1733 {
1734
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 1072 if(indentedChild.tagName() != "cls")
1735 {
1736 ✗ qCritical()
1737 ✗ << "Failed to load PolChemDef file: <cls> element not found.";
1738 ✗ return false;
1739 }
1740
1741
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 536 CleavageAgentSPtr cleavage_agent_sp = std::make_shared<CleavageAgent>(
1742 536 pol_chem_def_sp, indentedChild, version);
1743
1744
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 536 if(!cleavage_agent_sp->isValid())
1745 {
1746 ✗ qCritical() << "Failed to render the CleaveSpec instance from an "
1747 ✗ "XML <cls> element.";
1748 ✗ cleavage_agent_sp.reset();
1749 ✗ return false;
1750 }
1751
1752 // qDebug() << "Rendered CleavageAgent: " << cleavage_agent_sp->getName()
1753 // << "with pattern:" << cleavage_agent_sp->getPattern();
1754
1755
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 536 pol_chem_def_sp->m_cleavageAgents.push_back(cleavage_agent_sp);
1756
1757
1758
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 1072 indentedChild = indentedChild.nextSiblingElement();
1759 536 }
1760
1761 // qDebug() << "Size of CleavageAgent container:"
1762 // << pol_chem_def_sp->getCleavageAgentsCstRef().size()
1763 // << "pol chem def usage:" << pol_chem_def_sp.use_count();
1764
1765 // qDebug() << "Now starting the rendering of the <fragspecs> element.";
1766
1767 // <fragspecs>
1768
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 134 child = child.nextSiblingElement();
1769
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 134 if(child.tagName() != "fragspecs")
1770 {
1771 ✗ qCritical()
1772 ✗ << "Failed to load PolChemDef file: <fragspecs> element not found.";
1773 ✗ return false;
1774 }
1775
1776
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 134 indentedChild = child.firstChildElement();
1777
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 536 while(!indentedChild.isNull())
1778 {
1779
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 938 if(indentedChild.tagName() != "fgs")
1780 {
1781 ✗ qCritical()
1782 ✗ << "Failed to load PolChemDef file: <fgs> element not found.";
1783 ✗ return false;
1784 }
1785
1786
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 469 FragmentationPathwaySPtr fragmentation_pathway_sp =
1787 std::make_shared<FragmentationPathway>(
1788 469 pol_chem_def_sp, indentedChild, version);
1789
1790
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 469 if(!fragmentation_pathway_sp->isValid())
1791 {
1792 ✗ qCritical() << "Failed to render the FragSpec instance from an "
1793 ✗ "XML <fgs> element.";
1794 ✗ fragmentation_pathway_sp.reset();
1795 ✗ return false;
1796 }
1797
1798 469 qDebug() << "Rendered FragmentationPathway: "
1799 << fragmentation_pathway_sp->getName();
1800
1801
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 469 pol_chem_def_sp->m_fragmentationPathways.push_back(
1802 fragmentation_pathway_sp);
1803
1804
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 938 indentedChild = indentedChild.nextSiblingElement();
1805 469 }
1806
1807 // qDebug() << "Size of FragmentationPathway container:"
1808 // << pol_chem_def_sp->getFragmentationPathwaysCstRef().size()
1809 // << "pol chem def usage:" << pol_chem_def_sp.use_count();
1810
1811 // qDebug() << "Done rendering the PolChemDef file. Setting m_isValid to true "
1812 // "and returning it.";
1813
1814 67 pol_chem_def_sp->m_isValid = true;
1815
1816 67 return pol_chem_def_sp->m_isValid;
1817 134 }
1818
1819 /*!
1820 \brief Parses the polymer chemistry definition file and updates \a
1821 pol_chem_def_sp accordingly.
1822
1823 Upon parsing of the file and validation of the data, the \a
1824 pol_chem_def_sp is updated, essentially initializing it with the data from
1825 the file.
1826
1827 Note that the \a pol_chem_def_sp should have a working set of isotopic
1828 data.
1829
1830 Returns true if the parsing was successful and false otherwise.
1831 */
1832 bool
1833 1 PolChemDef::renderXmlPolChemDefFileVersion2(PolChemDefSPtr pol_chem_def_sp)
1834 {
1835 // qDebug() << "Rendering PolChemDef file VERSION 2.";
1836
1837
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 1 if(pol_chem_def_sp == nullptr && pol_chem_def_sp.get() == nullptr)
1838 ✗ qFatalStream()
1839 ✗ << "Programming error. The PolChemDef pointer cannot be nullptr.";
1840
1841 // qDebug() << "The PolChemDef *:" << pol_chem_def_sp.get()
1842 //<< "and usage:" << pol_chem_def_sp.use_count();
1843
1844 ///////////////////// ATTENTION ///////////////////
1845 // Before reading the polymer chemistry data file, we need to make sure
1846 // we actually have read the isotopic data!
1847
1848 // qDebug() << "First check if we have isotopic data ready.";
1849
1850
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 2 if(pol_chem_def_sp->getIsotopicDataSPtr() == nullptr)
1851 {
1852 // qDebug() << "No isotopic data found in the polymer chemistry "
1853 // "definition, need to load the data.";
1854
1855 // First read the data!
1856 ✗ std::size_t count = pol_chem_def_sp->loadIsotopicData(pol_chem_def_sp);
1857
1858 ✗ if(!count)
1859 ✗ qFatal("Programming error. The isotopic data could not be loaded.");
1860
1861 // qDebug() << "At this point the isotopic data were loaded fine
1862 // with"
1863 //<< count << "isotopes loaded.";
1864 }
1865
1866
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 1 QDomDocument doc("polChemDefData");
1867
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 1 QDomElement element;
1868
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 1 QDomElement child;
1869
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 1 QDomElement indentedChild;
1870
1871
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 1 QFile file(pol_chem_def_sp->m_xmlDataFilePath);
1872
1873 // qDebug() << "The polymer chemistry definition file:"
1874 // << pol_chem_def_sp->m_xmlDataFilePath;
1875
1876 // The general structure of the file we are reading is this:
1877 //
1878 // <polchemdefinition version="1">
1879 // <polchemdefdata">
1880 // <name>protein</name>
1881 // <leftcap>+H</leftcap>
1882 // <rightcap>+OH</rightcap>
1883 // <codelen>1</codelen>
1884 // <ionizerule>
1885 // <formula>+H</formula>
1886 // <charge>1</charge>
1887 // <level>1</level>
1888 // </ionizerule>
1889 // <monomers>
1890 // <mnm>
1891 // <name>Glycine</name>
1892 // <code>G</code>
1893 // <formula>C2H3NO</formula>
1894 // </mnm>
1895 // </monomers>
1896 // <modifs>
1897 // <mdf>
1898 // <name>Phosphorylation</name>
1899 // <formula>-H+H2PO3</formula>
1900 // </mdf>
1901 // </modifs>
1902 // <cleavageagents>
1903 // <cla>
1904 // <name>CyanogenBromide</name>
1905 // <pattern>M/</pattern>
1906 // <clr>
1907 // <re-mnm-code>M</re-mnm-code>
1908 // <re-formula>-CH2S+O</re-formula>
1909 // </clr>
1910 // </cla>
1911 // </cleavageagents>
1912 // <fragmentationpathways>
1913 // <fgp>
1914 // <name>a</name>
1915 // <end>LE</end>
1916 // <formula>-C1O1</formula>
1917 // <fgr>
1918 // <name>a-fgr-1</name>
1919 // <formula>+H200</formula>
1920 // <prev-mnm-code>E</prev-mnm-code>
1921 // <this-mnm-code>D</this-mnm-code>
1922 // <next-mnm-code>F</next-mnm-code>
1923 // <comment>comment here!</comment>
1924 // </fgr>
1925 // </fgp>
1926 // </fragmentationpathways>
1927 // </polchemdefdata>
1928 // </polchemdefinition>
1929
1930
1931
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 1 if(!file.open(QIODevice::ReadOnly))
1932 return false;
1933
1934
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 1 if(!doc.setContent(&file))
1935 {
1936 ✗ qDebug() << "Failed to set doc content.";
1937
1938 ✗ file.close();
1939 return false;
1940 }
1941
1942
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 1 file.close();
1943
1944 // qDebug() << "Closed the polymer chemistry definition file.";
1945
1946
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 1 element = doc.documentElement();
1947
1948
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 2 if(element.tagName() != "polchemdefinition")
1949 {
1950 qDebug() << "Polymer chemistry definition file is erroneous\n";
1951 return false;
1952 }
1953
1954 ///////////////////////////////////////////////
1955 // Check the version of the document.
1956
1957 1 QString text;
1958
1959
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 1 if(!element.hasAttribute("version"))
1960 ✗ text = "1";
1961 else
1962
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 1 text = element.attribute("version");
1963
1964 // qDebug() << "The format of the definition:" << text;
1965
1966 1 bool ok = false;
1967
1968
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 1 int version = text.toInt(&ok, 10);
1969
1970
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 1 if(version != 2 || !ok)
1971 {
1972 // qDebug() << "Polymer chemistry definition file has bad "
1973 // "version number:"
1974 // << version;
1975
1976 return false;
1977 }
1978
1979 //////////////////////////////////////////////
1980 // <polymer chemistry data>
1981
1982
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 2 child = element.firstChildElement();
1983
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 2 if(child.tagName() != "polchemdefdata")
1984 {
1985 qDebug() << "Polymer chemistry definition file is erroneous\n";
1986 return false;
1987 }
1988
1989 // <name>
1990
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1991
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 2 if(child.tagName() != "name")
1992 return false;
1993
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 1 pol_chem_def_sp->m_name = child.text();
1994
1995 // <leftcap>
1996
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1997
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 2 if(child.tagName() != "leftcap")
1998 return false;
1999
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 1 pol_chem_def_sp->m_leftCap.setActionFormula(child.text());
2000
2001 // <rightcap>
2002
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2003
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 2 if(child.tagName() != "rightcap")
2004 return false;
2005
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 1 pol_chem_def_sp->m_rightCap.setActionFormula(child.text());
2006
2007 // <codelen>
2008
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 2 child = child.nextSiblingElement();
2009
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 2 if(child.tagName() != "codelen")
2010 return false;
2011 1 ok = false;
2012
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 2 pol_chem_def_sp->m_codeLength = child.text().toInt(&ok);
2013
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 1 if(pol_chem_def_sp->m_codeLength == 0 && !ok)
2014 return false;
2015 // qDebug() << "Set the code length to" << pol_chem_def_sp->m_codeLength;
2016
2017 // <ionizerule>
2018
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 2 child = child.nextSiblingElement();
2019
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 2 if(child.tagName() != "ionizerule")
2020 return false;
2021
2022 // It is essential that we endow the Ionizer with the IsotopicData !
2023
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 1 pol_chem_def_sp->m_ionizer.setIsotopicDataCstSPtr(
2024
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 1 pol_chem_def_sp->getIsotopicDataCstSPtr());
2025
2026 // Now we can render the Ionizer by looking into the <ionizerule> XML
2027 // element.
2028
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 1 if(!pol_chem_def_sp->m_ionizer.renderXmlIonizeRuleElement(child))
2029 return false;
2030
2031 // Finally, we have to ascertain that the Ionizer is valid.
2032 1 ErrorList error_list;
2033
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 1 if(!pol_chem_def_sp->m_ionizer.validate(&error_list))
2034 {
2035 ✗ qCritical() << "The Ionizer is invalid, with errors:"
2036 ✗ << Utils::joinErrorList(error_list, ", ");
2037 ✗ return false;
2038 }
2039
2040 // qDebug() << "Now starting the rendering of the <monomers> element.";
2041
2042 // <monomers>
2043
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2044
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 2 if(child.tagName() != "monomers")
2045 return false;
2046
2047
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 2 indentedChild = child.firstChildElement();
2048
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 22 while(!indentedChild.isNull())
2049 {
2050 // qDebug() << "Now rendering one of all the mnm elements.";
2051
2052
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 42 if(indentedChild.tagName() != "mnm")
2053 {
2054 ✗ qCritical() << "The expected <mnm> element was not found.";
2055 ✗ return false;
2056 }
2057
2058 // Constructing a Monomer using the XML element ensures
2059 // that the masses are properly calculated for it, so
2060 // that MonomerCstSPtr point to fully qualified Monomer
2061 // instances that properly play the role of reference
2062 // throughout the chemical entities that involve Monomer
2063 // instances in the context of this PolChemDef.
2064
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 21 MonomerSPtr monomer_sp =
2065 21 std::make_shared<Monomer>(pol_chem_def_sp, indentedChild, version);
2066
2067
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 21 if(!monomer_sp->isValid())
2068 {
2069 ✗ qDebug() << "Failed to render mnm element.";
2070
2071 ✗ monomer_sp.reset();
2072 ✗ return false;
2073 }
2074
2075
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 21 pol_chem_def_sp->m_monomers.push_back(monomer_sp);
2076
2077
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 42 indentedChild = indentedChild.nextSiblingElement();
2078 21 }
2079
2080 // qDebug() << "Size of MonomerList:"
2081 // << pol_chem_def_sp->getMonomersCstRef().size()
2082 // << "pol chem def usage:" << pol_chem_def_sp.use_count();
2083
2084 // qDebug() << "Now starting the rendering of the <modifs> element.";
2085
2086 // <modifs>
2087
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2088
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 2 if(child.tagName() != "modifs")
2089 return false;
2090
2091
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 2 indentedChild = child.firstChildElement();
2092
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 27 while(!indentedChild.isNull())
2093 {
2094
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 52 if(indentedChild.tagName() != "mdf")
2095 ✗ return false;
2096
2097
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 26 ModifSPtr modif_sp =
2098 26 std::make_shared<Modif>(pol_chem_def_sp, indentedChild, version);
2099
2100
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 26 if(!modif_sp->isValid())
2101 {
2102 ✗ qCritical()
2103 ✗ << "Failed to render the Modif instance from an XML <mdf> element.";
2104 ✗ modif_sp.reset();
2105 ✗ return false;
2106 }
2107
2108
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 26 pol_chem_def_sp->m_modifs.push_back(modif_sp);
2109
2110
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 52 indentedChild = indentedChild.nextSiblingElement();
2111 26 }
2112
2113 // qDebug() << "Size of ModifList:" << pol_chem_def_sp->getModifsCstRef().size()
2114 // << "pol chem def usage:" << pol_chem_def_sp.use_count();
2115
2116 // qDebug() << "Now starting the rendering of the <crosslinkers> element.";
2117
2118 // <crosslinkers>
2119 // Note that crosslinkers have appeared since version 3.
2120
2121
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2122
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 2 if(child.tagName() != "crosslinkers")
2123 return false;
2124
2125
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2126
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 3 while(!indentedChild.isNull())
2127 {
2128
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 4 if(indentedChild.tagName() != "clk")
2129 ✗ return false;
2130
2131
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 2 CrossLinkerSPtr crossLinker_sp =
2132 2 std::make_shared<CrossLinker>(pol_chem_def_sp, indentedChild, version);
2133
2134
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 2 if(!crossLinker_sp->isValid())
2135 {
2136 ✗ qCritical() << "Failed to render the CrossLinker instance from an "
2137 ✗ "XML <clk> element.";
2138 ✗ crossLinker_sp.reset();
2139 ✗ return false;
2140 }
2141
2142
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 2 pol_chem_def_sp->m_crossLinkers.push_back(crossLinker_sp);
2143
2144 // qDebug() << "Rendered CrossLinker: " << crossLinker_csp->getName()
2145 // << "with formula:" << crossLinker_csp->getFormula()
2146 // << "with masses:" <<
2147 // crossLinker_csp->getMass(Enums::MassType::MONO)
2148 // << "/" << crossLinker_csp->getMass(Enums::MassType::AVG);
2149
2150
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 4 indentedChild = indentedChild.nextSiblingElement();
2151 2 }
2152
2153 // qDebug() << "Size of CrossLinker container:"
2154 // << pol_chem_def_sp->getCrossLinkersCstRef().size()
2155 // << "pol chem def usage:" << pol_chem_def_sp.use_count();
2156
2157 // qDebug() << "Now starting the rendering of the <cleavageagents> element.";
2158
2159 // <cleavageagents>
2160
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 2 child = child.nextSiblingElement();
2161
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 2 if(child.tagName() != "cleavageagents")
2162 {
2163 ✗ qCritical() << "Failed to load PolChemDef file: <cleavageagents> element "
2164 ✗ "not found.";
2165 ✗ return false;
2166 }
2167
2168
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 2 indentedChild = child.firstChildElement();
2169
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 9 while(!indentedChild.isNull())
2170 {
2171
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 16 if(indentedChild.tagName() != "cla")
2172 {
2173 ✗ qCritical()
2174 ✗ << "Failed to load PolChemDef file: <cla> element not found.";
2175 ✗ return false;
2176 }
2177
2178 // qDebug() << "Will allocate a new CleavageAgent instance->shared pointer.";
2179
2180
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 8 CleavageAgentSPtr cleavage_agent_sp = std::make_shared<CleavageAgent>(
2181 8 pol_chem_def_sp, indentedChild, version);
2182
2183
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 8 if(!cleavage_agent_sp->isValid())
2184 {
2185 ✗ qCritical() << "Failed to render the CleavageAgent instance from an "
2186 ✗ "XML <cla> element.";
2187 ✗ cleavage_agent_sp.reset();
2188 ✗ return false;
2189 }
2190
2191
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 8 pol_chem_def_sp->m_cleavageAgents.push_back(cleavage_agent_sp);
2192
2193
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 16 indentedChild = indentedChild.nextSiblingElement();
2194 8 }
2195
2196 // qDebug() << "Size of CleavageAgent container:"
2197 // << pol_chem_def_sp->getCleavageAgentsCstRef().size()
2198 // << "pol chem def usage:" << pol_chem_def_sp.use_count();
2199
2200 // qDebug()
2201 // << "Now starting the rendering of the <fragmentationpathways> element.";
2202
2203 // <fragmentationpathways>
2204
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2205
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 2 if(child.tagName() != "fragmentationpathways")
2206 return false;
2207
2208
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2209
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 8 while(!indentedChild.isNull())
2210 {
2211
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 14 if(indentedChild.tagName() != "fgp")
2212 {
2213 ✗ qCritical()
2214 ✗ << "Failed to load PolChemDef file: <fgp> element not found.";
2215 ✗ return false;
2216 }
2217
2218
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 7 FragmentationPathwaySPtr fragmentation_pathway_sp =
2219 std::make_shared<FragmentationPathway>(
2220 7 pol_chem_def_sp, indentedChild, version);
2221
2222
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 7 if(!fragmentation_pathway_sp->isValid())
2223 {
2224 ✗ qCritical()
2225 << "Failed to render the FragmentationPathway instance from an "
2226 ✗ "XML <fgs> element.";
2227 ✗ fragmentation_pathway_sp.reset();
2228 ✗ return false;
2229 }
2230
2231
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 7 pol_chem_def_sp->m_fragmentationPathways.push_back(
2232 fragmentation_pathway_sp);
2233
2234
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 14 indentedChild = indentedChild.nextSiblingElement();
2235 7 }
2236
2237 // qDebug() << "Size of FragmentationPathway container:"
2238 // << pol_chem_def_sp->getFragmentationPathwaysCstRef().size()
2239 // << "pol chem def usage:" << pol_chem_def_sp.use_count();
2240
2241 // qDebug() << "Done rendering the PolChemDef file. Setting m_isValid to true "
2242 // "and returning it.";
2243
2244 1 pol_chem_def_sp->m_isValid = true;
2245
2246 1 return pol_chem_def_sp->m_isValid;
2247 2 }
2248
2249 /*!
2250 \brief Parses the polymer chemistry definition file and updates \a
2251 pol_chem_def_sp accordingly.
2252
2253 Upon parsing of the file and validation of the data, the \a
2254 pol_chem_def_sp is updated, essentially initializing it with the data from
2255 the file.
2256
2257 Note that the \a pol_chem_def_sp should have a working set of isotopic
2258 data.
2259
2260 Returns true if the parsing was successful and false otherwise.
2261 */
2262 bool
2263 68 PolChemDef::renderXmlPolChemDefFile(PolChemDefSPtr pol_chem_def_sp)
2264 {
2265
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 68 if(pol_chem_def_sp == nullptr && pol_chem_def_sp.get() == nullptr)
2266 ✗ qFatalStream()
2267 ✗ << "Programming error. The PolChemDef pointer cannot be nullptr.";
2268
2269 // qDebug() << "The PolChemDef *:" << pol_chem_def_sp.get()
2270 //<< "and usage:" << pol_chem_def_sp.use_count();
2271
2272 ///////////////////// ATTENTION ///////////////////
2273 // Before reading the polymer chemistry data file, we need to make sure
2274 // we actually have read the isotopic data!
2275
2276 // qDebug() << "First check if we have isotopic data ready.";
2277
2278
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 136 if(pol_chem_def_sp->getIsotopicDataSPtr() == nullptr)
2279 {
2280 // qDebug() << "No isotopic data found in the polymer chemistry "
2281 // "definition, need to load the data.";
2282
2283 // First read the data!
2284 ✗ std::size_t count = pol_chem_def_sp->loadIsotopicData(pol_chem_def_sp);
2285
2286 ✗ if(!count)
2287 ✗ qFatal("Programming error. The isotopic data could not be loaded.");
2288
2289 // qDebug() << "At this point the isotopic data were loaded fine
2290 // with"
2291 //<< count << "isotopes loaded.";
2292 }
2293
2294
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 68 QDomDocument doc("polChemDefData");
2295
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 68 QDomElement element;
2296
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 68 QDomElement child;
2297
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 68 QDomElement indentedChild;
2298
2299
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 68 QFile file(pol_chem_def_sp->m_xmlDataFilePath);
2300
2301 // qDebug() << "The polymer chemistry definition file:"
2302 // << pol_chem_def_sp->m_xmlDataFilePath;
2303
2304 // The general structure of the file we are reading is this:
2305 //
2306 // <polchemdefinition version="1">
2307 // <polchemdefdata">
2308 // <name>protein</name>
2309 // <leftcap>+H</leftcap>
2310 // <rightcap>+OH</rightcap>
2311 // <codelen>1</codelen>
2312 // <ionizerule>
2313 // <formula>+H</formula>
2314 // <charge>1</charge>
2315 // <level>1</level>
2316 // </ionizerule>
2317 // <monomers>
2318 // <mnm>
2319 // <name>Glycine</name>
2320 // <code>G</code>
2321 // <formula>C2H3NO</formula>
2322 // </mnm>
2323 // </monomers>
2324 // <modifs>
2325 // <mdf>
2326 // <name>Phosphorylation</name>
2327 // <formula>-H+H2PO3</formula>
2328 // </mdf>
2329 // </modifs>
2330 // <cleavageagents>
2331 // <cla>
2332 // <name>CyanogenBromide</name>
2333 // <pattern>M/</pattern>
2334 // <clr>
2335 // <re-mnm-code>M</re-mnm-code>
2336 // <re-formula>-CH2S+O</re-formula>
2337 // </clr>
2338 // </cla>
2339 // </cleavageagents>
2340 // <fragmentationpathways>
2341 // <fgp>
2342 // <name>a</name>
2343 // <end>LE</end>
2344 // <formula>-C1O1</formula>
2345 // <fgr>
2346 // <name>a-fgr-1</name>
2347 // <formula>+H200</formula>
2348 // <prev-mnm-code>E</prev-mnm-code>
2349 // <this-mnm-code>D</this-mnm-code>
2350 // <next-mnm-code>F</next-mnm-code>
2351 // <comment>comment here!</comment>
2352 // </fgr>
2353 // </fgp>
2354 // </fragmentationpathways>
2355 // </polchemdefdata>
2356 // </polchemdefinition>
2357
2358
2359
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 68 if(!file.open(QIODevice::ReadOnly))
2360 return false;
2361
2362
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 68 if(!doc.setContent(&file))
2363 {
2364 ✗ qDebug() << "Failed to set doc content.";
2365
2366 ✗ file.close();
2367 return false;
2368 }
2369
2370
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 68 file.close();
2371
2372 // qDebug() << "Closed the polymer chemistry definition file.";
2373
2374
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 68 element = doc.documentElement();
2375
2376
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 136 if(element.tagName() != "polchemdefinition")
2377 {
2378 qDebug() << "Polymer chemistry definition file is erroneous\n";
2379 return false;
2380 }
2381
2382 ///////////////////////////////////////////////
2383 // Check the version of the document.
2384
2385 68 QString text;
2386
2387
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 68 if(!element.hasAttribute("version"))
2388 ✗ text = "1";
2389 else
2390
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 68 text = element.attribute("version");
2391
2392 // qDebug() << "The format of the definition:" << text;
2393
2394 68 bool ok = false;
2395
2396
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 68 int version = text.toInt(&ok, 10);
2397
2398
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 68 if(version < 1 || !ok)
2399 {
2400 ✗ qDebug() << "Polymer chemistry definition file has bad "
2401 "version number:"
2402 << version;
2403
2404 ✗ return false;
2405 }
2406
2407 //FIXME, done already file.close();
2408
2409 // qDebug() << "The version of the Polymer Chemistry Definition file is:"
2410 // << version;
2411
2412
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 68 if(version == 1)
2413
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 134 return PolChemDef::renderXmlPolChemDefFileVersion1(pol_chem_def_sp);
2414
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 1 else if(version == 2)
2415
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 2 return PolChemDef::renderXmlPolChemDefFileVersion2(pol_chem_def_sp);
2416
2417 return false;
2418 68 }
2419
2420 /*!
2421 \brief Returns a string with the XML DTD for a polymer chemistry
2422 definition file.
2423 */
2424 QString
2425 1 PolChemDef::formatXmlDtd()
2426 {
2427 1 QString string = QString(
2428 "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>\n"
2429 "<!-- DTD for polymer definitions, used by the\n"
2430 "'massXpert' mass spectrometry application.\n"
2431 "Copyright 2006,2007,2008 Filippo Rusconi\n"
2432 "Licensed under the GNU GPL -->\n"
2433 "<!DOCTYPE polchemdefinition [\n"
2434 "<!ELEMENT polchemdefinition (polchemdefdata)>\n"
2435 "<!ATTLIST polchemdefinition version NMTOKEN #REQUIRED>\n"
2436 "<!ELEMENT polchemdefdata "
2437 "(name,leftcap,rightcap,codelen,ionizerule,monomers,modifs,"
2438 "crosslinkers,"
2439 "cleavageagents,fragmentationpathways)>\n"
2440 "<!ELEMENT ionizerule (formula,charge,level)>\n"
2441 "<!ELEMENT monomers (mnm*)>\n"
2442 "<!ELEMENT modifs (mdf*)>\n"
2443 "<!ELEMENT crosslinkers (clk*)>\n"
2444 "<!ELEMENT cleavageagents (cla*)>\n"
2445 "<!ELEMENT fragmentationpathways (fgp*)>\n"
2446 "<!ELEMENT mnm (name,code,formula)>\n"
2447 "<!ELEMENT mdf (name,formula,targets,maxcount)>\n"
2448 "<!ELEMENT clk (name,formula,modifname*)>\n"
2449 "<!ELEMENT cla (name,pattern,clr*)>\n"
2450 "<!ELEMENT fgp (name,end,formula,sidechaincontrib,comment?,fgr*)>\n"
2451 "<!ELEMENT clr "
2452 "(name,(le-mnm-code,le-formula)?,(re-mnm-code,re-formula)?)>\n"
2453 "<!ELEMENT fgr "
2454 "(name,formula,prev-mnm-code?,curr-mnm-code?,next-mnm-code?,comment?)"
2455 ">\n"
2456 "<!ELEMENT leftcap (#PCDATA)>\n"
2457 "<!ELEMENT rightcap (#PCDATA)>\n"
2458 "<!ELEMENT codelen (#PCDATA)>\n"
2459 "<!ELEMENT charge (#PCDATA)>\n"
2460 "<!ELEMENT maxcount (#PCDATA)>\n"
2461 "<!ELEMENT level (#PCDATA)>\n"
2462 "<!ELEMENT name (#PCDATA)>\n"
2463 "<!ELEMENT modifname (#PCDATA)>\n"
2464 "<!ELEMENT code (#PCDATA)>\n"
2465 "<!ELEMENT formula (#PCDATA)>\n"
2466 "<!ELEMENT sidechaincontrib (#PCDATA)>\n"
2467 "<!ELEMENT targets (#PCDATA)>\n"
2468 "<!ELEMENT pattern (#PCDATA)>\n"
2469 "<!ELEMENT end (#PCDATA)>\n"
2470 "<!ELEMENT le-mnm-code (#PCDATA)>\n"
2471 "<!ELEMENT re-mnm-code (#PCDATA)>\n"
2472 "<!ELEMENT le-formula (#PCDATA)>\n"
2473 "<!ELEMENT re-formula (#PCDATA)>\n"
2474 "<!ELEMENT comment (#PCDATA)>\n"
2475 "<!ELEMENT prev-mnm-code (#PCDATA)>\n"
2476 "<!ELEMENT curr-mnm-code (#PCDATA)>\n"
2477 "<!ELEMENT next-mnm-code (#PCDATA)>\n"
2478 1 "]>\n");
2479
2480 1 return string;
2481 }
2482
2483 /*!
2484 \brief Writes the polymer chemistry definition to file.
2485
2486 The file's name is from m_xmlDataFilePath.
2487
2488 Returns true if successful, false otherwise.
2489 */
2490 bool
2491 1 PolChemDef::writeXmlFile()
2492 {
2493 1 QString indent(" ");
2494 1 QString lead;
2495
2496 1 int offset = 0;
2497 1 int iter = 0;
2498
2499 // We are asked to send an xml description of the polymer chemistry
2500 // definition.
2501
2502
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 1 QFile file(m_xmlDataFilePath);
2503
2504
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 1 if(!file.open(QIODevice::WriteOnly))
2505 {
2506 qDebug() << "Failed to open file" << m_xmlDataFilePath << "for writing.";
2507
2508 return false;
2509 }
2510
2511
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 1 QTextStream stream(&file);
2512
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 1 stream.setEncoding(QStringConverter::Utf8);
2513
2514 // The DTD
2515
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 1 stream << formatXmlDtd();
2516
2517
2518 // Open the <polchemdefinition> element.
2519
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 1 stream << QString("<polchemdefinition version=\"%1\">\n")
2520
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 2 .arg(POL_CHEM_DEF_FILE_FORMAT_VERSION);
2521
2522 // Prepare the lead.
2523 1 ++offset;
2524 1 lead.clear();
2525 1 iter = 0;
2526 1 while(iter < offset)
2527 {
2528
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 2 lead += indent;
2529 ++iter;
2530 }
2531
2532 // Open the <polchemdefdata> element.
2533
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 2 stream << QString("%1<polchemdefdata>\n").arg(lead);
2534
2535 // Prepare the lead.
2536 1 ++offset;
2537 1 lead.clear();
2538 1 iter = 0;
2539
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 4 while(iter < offset)
2540 {
2541
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 2 lead += indent;
2542 2 ++iter;
2543 }
2544
2545
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 2 stream << QString("%1<name>%2</name>\n").arg(lead).arg(m_name);
2546
2547
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 1 stream << QString("%1<leftcap>%2</leftcap>\n")
2548
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 2 .arg(lead)
2549
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 2 .arg(m_leftCap.getActionFormula(/*with_title*/ true));
2550
2551
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 1 stream << QString("%1<rightcap>%2</rightcap>\n")
2552
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 2 .arg(lead)
2553
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 2 .arg(m_rightCap.getActionFormula(/*with_title*/ true));
2554
2555
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 2 stream << QString("%1<codelen>%2</codelen>\n").arg(lead).arg(m_codeLength);
2556
2557 // Before writing the ionization rule, set the level to 1. This
2558 // member datum is set to 0 in the constructor.
2559
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 1 m_ionizer.setLevel(1);
2560
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 1 stream << m_ionizer.formatXmlIonizeRuleElement(offset);
2561
2562
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 2 stream << QString("%1<monomers>\n").arg(lead);
2563
2564 // Prepare the lead.
2565 1 ++offset;
2566 1 lead.clear();
2567 1 iter = 0;
2568
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 5 while(iter < offset)
2569 {
2570
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 3 lead += indent;
2571 3 ++iter;
2572 }
2573
2574
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 22 for(const auto &monomer_csp : m_monomers)
2575
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 42 stream << monomer_csp->formatXmlMnmElement(offset);
2576
2577 // Prepare the lead.
2578 1 --offset;
2579 1 lead.clear();
2580 1 iter = 0;
2581
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 4 while(iter < offset)
2582 {
2583
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 2 lead += indent;
2584 2 ++iter;
2585 }
2586
2587
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 2 stream << QString("%1</monomers>\n").arg(lead);
2588
2589
2590
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 2 stream << QString("%1<modifs>\n").arg(lead);
2591
2592 // Prepare the lead.
2593 1 ++offset;
2594 1 lead.clear();
2595 1 iter = 0;
2596
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 5 while(iter < offset)
2597 {
2598
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 3 lead += indent;
2599 3 ++iter;
2600 }
2601
2602
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 27 for(const auto &modif_csp : m_modifs)
2603
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 52 stream << modif_csp->formatXmlMdfElement(offset);
2604
2605 // Prepare the lead.
2606 1 --offset;
2607 1 lead.clear();
2608 1 iter = 0;
2609
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 4 while(iter < offset)
2610 {
2611
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 2 lead += indent;
2612 2 ++iter;
2613 }
2614
2615
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 2 stream << QString("%1</modifs>\n").arg(lead);
2616
2617
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 2 stream << QString("%1<crosslinkers>\n").arg(lead);
2618
2619 // Prepare the lead.
2620 1 ++offset;
2621 1 lead.clear();
2622 1 iter = 0;
2623
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 5 while(iter < offset)
2624 {
2625
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 3 lead += indent;
2626 3 ++iter;
2627 }
2628
2629
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 3 for(const auto &cross_linker_csp : m_crossLinkers)
2630
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 4 stream << cross_linker_csp->formatXmlClkElement(offset);
2631
2632 // Prepare the lead.
2633 1 --offset;
2634 1 lead.clear();
2635 1 iter = 0;
2636
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 4 while(iter < offset)
2637 {
2638
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 2 lead += indent;
2639 2 ++iter;
2640 }
2641
2642
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 2 stream << QString("%1</crosslinkers>\n").arg(lead);
2643
2644
2645
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 2 stream << QString("%1<cleavageagents>\n").arg(lead);
2646
2647 // Prepare the lead.
2648 1 ++offset;
2649 1 lead.clear();
2650 1 iter = 0;
2651
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 5 while(iter < offset)
2652 {
2653
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 3 lead += indent;
2654 3 ++iter;
2655 }
2656
2657
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 9 for(const auto &cleavage_agent_csp : m_cleavageAgents)
2658
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 16 stream << cleavage_agent_csp->formatXmlClaElement(offset);
2659
2660 // Prepare the lead.
2661 1 --offset;
2662 1 lead.clear();
2663 1 iter = 0;
2664
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 4 while(iter < offset)
2665 {
2666
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 2 lead += indent;
2667 2 ++iter;
2668 }
2669
2670
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 2 stream << QString("%1</cleavageagents>\n").arg(lead);
2671
2672
2673
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 2 stream << QString("%1<fragmentationpathways>\n").arg(lead);
2674
2675
2676 // Prepare the lead.
2677 1 ++offset;
2678 1 lead.clear();
2679 1 iter = 0;
2680
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 5 while(iter < offset)
2681 {
2682
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 3 lead += indent;
2683 3 ++iter;
2684 }
2685
2686
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 8 for(const auto &fragmentation_pathway_csp : m_fragmentationPathways)
2687
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 14 stream << fragmentation_pathway_csp->formatXmlFgpElement(offset);
2688
2689 // Prepare the lead.
2690 1 --offset;
2691 1 lead.clear();
2692 1 iter = 0;
2693
2/2
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 4 while(iter < offset)
2694 {
2695
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 2 lead += indent;
2696 2 ++iter;
2697 }
2698
2699
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 2 stream << QString("%1</fragmentationpathways>\n").arg(lead);
2700
2701 // Prepare the lead.
2702 1 --offset;
2703 1 lead.clear();
2704 1 iter = 0;
2705 1 while(iter < offset)
2706 {
2707
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 2 lead += indent;
2708 ++iter;
2709 }
2710
2711
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 2 stream << QString("%1</polchemdefdata>\n").arg(lead);
2712
2713 // Prepare the lead.
2714 1 --offset;
2715 1 lead.clear();
2716 1 iter = 0;
2717 1 while(iter < offset)
2718 {
2719 lead += indent;
2720 ++iter;
2721 }
2722
2723
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 2 stream << QString("%1</polchemdefinition>\n").arg(lead);
2724
2725
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 1 file.close();
2726
2727 1 return true;
2728 1 }
2729
2730 /*!
2731 \brief Validates this PolChemDef instance by checking the validity of all its
2732 members data. Returns true if validation was successful, false otherwise. Any
2733 error is added to \a error_list_p if non-nullptr.
2734 */
2735 bool
2736 55 PolChemDef::validate(ErrorList *error_list_p) const
2737 {
2738 // So we can return immediately upon error.
2739 55 m_isValid = false;
2740
2741
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✓ Branch 1 taken 55 times.
 55 if(m_isotopicDataFilePath.isEmpty())
2742 {
2743 ✗ if(error_list_p != nullptr)
2744 ✗ error_list_p->push_back("The IsotopicData file path is empty.");
2745 ✗ return false;
2746 }
2747
2748 55 QFileInfo file_info(m_isotopicDataFilePath);
2749
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 55 if(!file_info.exists())
2750 {
2751 ✗ if(error_list_p != nullptr)
2752 ✗ error_list_p->push_back("The IsotopicData file cannot be found.");
2753 ✗ return false;
2754 }
2755
2756
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 55 if(msp_isotopicData == nullptr || msp_isotopicData.get() == nullptr)
2757 {
2758 ✗ if(error_list_p != nullptr)
2759 ✗ error_list_p->push_back("The IsotopicData are not available.");
2760 ✗ return false;
2761 }
2762
2763
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 55 if(m_name.isEmpty())
2764 {
2765 ✗ if(error_list_p != nullptr)
2766 ✗ error_list_p->push_back("The PolChemDef name is empty.");
2767 ✗ return false;
2768 }
2769
2770
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 55 if(m_xmlDataFilePath.isEmpty())
2771 {
2772 ✗ if(error_list_p != nullptr)
2773 ✗ error_list_p->push_back("The PolChemDef file path is empty.");
2774 ✗ return false;
2775 }
2776
2777
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 55 file_info.setFile(m_xmlDataFilePath);
2778
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 55 if(!file_info.exists())
2779 {
2780 ✗ if(error_list_p != nullptr)
2781 ✗ error_list_p->push_back("The PolChemDef file cannot be found.");
2782 ✗ return false;
2783 }
2784
2785
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 110 if(!m_leftCap.validate(msp_isotopicData, error_list_p))
2786 {
2787 ✗ if(error_list_p != nullptr)
2788 ✗ error_list_p->push_back("The left cap formula failed to validate.");
2789 ✗ return false;
2790 }
2791
2792
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 110 if(!m_rightCap.validate(msp_isotopicData, error_list_p))
2793 {
2794 ✗ if(error_list_p != nullptr)
2795 ✗ error_list_p->push_back("The right cap formula failed to validate.");
2796 ✗ return false;
2797 }
2798
2799
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 55 if(m_codeLength < 1)
2800 {
2801 ✗ if(error_list_p != nullptr)
2802 ✗ error_list_p->push_back("The code length is less than 1.");
2803 ✗ return false;
2804 }
2805
2806
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 55 if(!m_ionizer.validate(error_list_p))
2807 {
2808 ✗ if(error_list_p != nullptr)
2809 ✗ error_list_p->push_back("The ionization rule failed to validate.");
2810 ✗ return false;
2811 }
2812
2813
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 55 if(!m_modifs.size())
2814 {
2815 ✗ if(error_list_p != nullptr)
2816 ✗ error_list_p->push_back("There is not a single Modif instance.");
2817 ✗ return false;
2818 }
2819
2820
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 55 if(!m_monomers.size())
2821 {
2822 ✗ if(error_list_p != nullptr)
2823 ✗ error_list_p->push_back("There is not a single Monomer instance.");
2824 ✗ return false;
2825 }
2826
2827 // Good!
2828 55 m_isValid = true;
2829 55 return m_isValid;
2830 55 }
2831
2832 /*!
2833 \brief Returns the validity status of thie PolChemDef instance.
2834 */
2835 bool
2836 26701 PolChemDef::isValid() const
2837 {
2838 26701 return m_isValid;
2839 }
2840
2841
2842 } // namespace libXpertMassCore
2843 } // namespace MsXpS
2844