GCC Code Coverage Report

source/XpertMassCore/src/
File: source/XpertMassCore/src/ChemicalGroup.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 /////////////////////// Local includes
35 #include "MsXpS/libXpertMassCore/ChemicalGroup.hpp"
36
37
38 namespace MsXpS
39 {
40
41 namespace libXpertMassCore
42 {
43
44
45 /*!
46 \class MsXpS::libXpertMassCore::ChemicalGroup
47 \inmodule libXpertMassCore
48 \ingroup PolChemDefBuildingdBlocks
49 \inheaderfile ChemicalGroup.hpp
50
51 \brief The ChemicalGroup class provides a model for specifying the
52 acido-basic behaviour of a chemical group of either a \l Monomer object or of a
53 \l Modif object.
54
55 If the ChemicalGroup does not prove sufficient to characterize precisely the
56 acido-basic properties of an entity, \l ChemicalGroupRule instances can be
57 added to that effect.
58
59 In an pkaphpidata definition file, the following xml structure
60 is encountered:
61
62 \code
63 <pkaphpidata>
64 <monomers>
65 <monomer>
66 <code>A</code>
67 <mnmchemgroup>
68 <name>N-term NH2</name>
69 <pka>9.6</pka>
70 <acidcharged>TRUE</acidcharged>
71 <polrule>left_trapped</polrule>
72 <chemgrouprule>
73 <entity>LE_PLM_MODIF</entity>
74 <name>Acetylation</name>
75 <outcome>LOST</outcome>
76 </chemgrouprule>
77 </mnmchemgroup>
78 <mnmchemgroup>
79 <name>C-term COOH</name>
80 <pka>2.35</pka>
81 <acidcharged>FALSE</acidcharged>
82 <polrule>right_trapped</polrule>
83 </mnmchemgroup>
84 </monomer>
85 <monomer>
86 <code>C</code>
87 <mnmchemgroup>
88 <name>N-term NH2</name>
89 <pka>9.6</pka>
90 <acidcharged>TRUE</acidcharged>
91 <polrule>left_trapped</polrule>
92 <chemgrouprule>
93 <entity>LE_PLM_MODIF</entity>
94 <name>Acetylation</name>
95 <outcome>LOST</outcome>
96 </chemgrouprule>
97 </mnmchemgroup>
98 <mnmchemgroup>
99 <name>C-term COOH</name>
100 <pka>2.35</pka>
101 <acidcharged>FALSE</acidcharged>
102 <polrule>right_trapped</polrule>
103 </mnmchemgroup>
104 <mnmchemgroup>
105 <name>Lateral SH2</name>
106 <pka>8.3</pka>
107 <acidcharged>FALSE</acidcharged>
108 <polrule>never_trapped</polrule>
109 </mnmchemgroup>
110 </monomer>
111 .....
112 <modifs>
113 <modif>
114 <name>Phosphorylation</name>
115 <mdfchemgroup>
116 <name>none_set</name>
117 <pka>1.2</pka>
118 <acidcharged>FALSE</acidcharged>
119 </mdfchemgroup>
120 <mdfchemgroup>
121 <name>none_set</name>
122 <pka>6.5</pka>
123 <acidcharged>FALSE</acidcharged>
124 </mdfchemgroup>
125 </modif>
126 </modifs>
127 </pkaphpidata>
128 \endcode
129
130 \sa ChemicalGroupRule,
131 */
132
133 /*!
134 \variable MsXpS::libXpertMassCore::ChemicalGroup::m_name
135
136 \brief The name of the ChemicalGroup instance.
137 */
138
139 /*!
140 \variable MsXpS::libXpertMassCore::ChemicalGroup::m_pka
141
142 \brief The pKa of the ChemicalGroup instance.
143 */
144
145 /*!
146 \variable MsXpS::libXpertMassCore::ChemicalGroup::m_acidCharged
147
148 \brief Tells if the group is charged when in acid conditions (that is, the pH
149 is less than the pKa).
150 */
151
152 /*!
153 \variable MsXpS::libXpertMassCore::ChemicalGroup::m_polymerizationRule
154
155 \brief The way this ChemicalGroup behaves upon polymerization of the chemical
156 entity into a \l Polymer.
157 */
158
159 /*!
160 \variable MsXpS::libXpertMassCore::ChemicalGroup::m_rules
161
162 \brief The container of \l ChemicalGroupRule instances.
163 */
164
165 /*!
166 \brief Constructs a ChemicalGroup instance.
167
168 \a name The name of this ChemicalGroup.
169 \a pka The pKa value of this ChemicalGroup.
170 \a is_acid_charged Tells if the ChemicalGroup bears a charge when in acidic
171 conditions.
172 \a polymerization_rule Specifies the polymerization rule.
173
174 Upon construction the object is validated and m_isValid is set to the result of
175 that validation.
176 */
177 7 ChemicalGroup::ChemicalGroup(const QString &name,
178 float pka,
179 bool is_acid_charged,
180 7 Enums::ChemicalGroupTrapped polymerization_rule)
181
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 7 : m_name(name),
182 7 m_pka(pka),
183 7 m_acidCharged(is_acid_charged),
184
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 7 m_polymerizationRule(polymerization_rule)
185 {
186 7 if(m_pka <= 0 && m_pka >= 14)
187 qFatalStream() << "Programming error. pKa cannot be <=0 or >= 14.";
188
189 7 ErrorList error_list;
190
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 7 m_isValid = validate(&error_list);
191
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 7 if(!m_isValid)
192
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 14 qCritical()
193
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 7 << "The ChemicalGroup right constructed did not validate successfully.";
194 7 }
195
196 /*!
197 \brief Construct a ChemicalGroup instance as a copy of \a other.
198
199 There is no checking of the validity of \a other.
200 */
201 1 ChemicalGroup::ChemicalGroup(const ChemicalGroup &other)
202
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 1 : m_name(other.m_name),
203 1 m_pka(other.m_pka),
204 1 m_acidCharged(other.m_acidCharged),
205 1 m_polymerizationRule(other.m_polymerizationRule),
206 1 m_isValid(other.m_isValid)
207 {
208 // We want a new allocation, not a shared pointer copy.
209
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 3 for(const ChemicalGroupRuleSPtr &chemical_group_rule_sp : other.m_rules)
210 4 m_rules.emplace_back(
211
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 4 std::make_shared<ChemicalGroupRule>(*chemical_group_rule_sp.get()));
212 1 }
213
214 /*!
215 \brief Destructs this ChemicalGroup instance.
216 */
217 8 ChemicalGroup::~ChemicalGroup()
218 {
219 8 }
220
221 /*!
222 \brief Assigns \a other to this ChemicalGroup instance.
223
224 \note The ChemicalGroupRule instances in \a other are deep-duplicated.
225
226 Returns a reference to this ChemicalGroup instance.
227 */
228 ChemicalGroup &
229 1 ChemicalGroup::operator=(const ChemicalGroup &other)
230 {
231
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 1 if(&other == this)
232 return *this;
233
234 1 m_name = other.m_name;
235 1 m_pka = other.m_pka;
236 1 m_acidCharged = other.m_acidCharged;
237 1 m_polymerizationRule = other.m_polymerizationRule;
238
239 // We want a new allocation, not a shared pointer copy.
240
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 3 for(const ChemicalGroupRuleSPtr &chemical_group_rule_sp : other.m_rules)
241 4 m_rules.emplace_back(
242
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 4 std::make_shared<ChemicalGroupRule>(*chemical_group_rule_sp.get()));
243
244 1 ErrorList error_list;
245
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 1 m_isValid = validate(&error_list);
246
247 1 return *this;
248 1 }
249
250 /*!
251 \brief Sets the \a name.
252 */
253 void
254 3 ChemicalGroup::setName(QString name)
255 {
256 3 m_name = name;
257
258 3 ErrorList error_list;
259
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 3 m_isValid = validate(&error_list);
260
261
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 3 if(!m_isValid)
262 {
263 ✗ qCritical()
264 ✗ << "After setting name, the object did not validate successfully.";
265 }
266 3 }
267
268 /*!
269 \brief Returns the name.
270 */
271 QString
272 3 ChemicalGroup::getName() const
273 {
274
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 3 return m_name;
275 }
276
277 /*!
278 \brief Sets the pKa to \a pka.
279 */
280 void
281 3 ChemicalGroup::setPka(float pka)
282 {
283 3 m_pka = pka;
284
285 3 ErrorList error_list;
286
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 3 m_isValid = validate(&error_list);
287
288
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 3 if(!m_isValid)
289 {
290 ✗ qCritical()
291 ✗ << "After setting pKa, the object did not validate successfully.";
292 }
293 3 }
294
295 /*!
296 \brief Returns the pKa.
297 */
298 float
299 3 ChemicalGroup::getPka() const
300 {
301 3 return m_pka;
302 }
303
304 /*!
305 \brief Sets the charge condition in acidic conditions to \a acid_charged.
306
307 If true, the group bears a charge when the pH is less than the pKa.
308 */
309 void
310 3 ChemicalGroup::setAcidCharged(bool acid_charged)
311 {
312 3 m_acidCharged = acid_charged;
313
314 3 ErrorList error_list;
315
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 3 m_isValid = validate(&error_list);
316
317
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 3 if(!m_isValid)
318 {
319 ✗ qCritical() << "After setting acid charged bool, the object did not "
320 ✗ "validate successfully.";
321 }
322 3 }
323
324 /*!
325 \brief Returns the charge condition in acidic conditions.
326
327 If true, the group bears a charge when the pH is less than the pKa.
328 */
329 bool
330 3 ChemicalGroup::isAcidCharged() const
331 {
332 3 return m_acidCharged;
333 }
334
335 /*!
336 \brief Sets the polymerization rule to \a pol_rule.
337
338 The polymerization rule determines if the chemical group is trapped upon
339 formation of a Monomer-to-Monomer bond.
340 */
341 void
342 3 ChemicalGroup::setPolRule(Enums::ChemicalGroupTrapped pol_rule)
343 {
344 3 m_polymerizationRule = pol_rule;
345
346 3 ErrorList error_list;
347
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 3 m_isValid = validate(&error_list);
348
349
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 3 if(!m_isValid)
350 {
351 ✗ qCritical() << "After setting Enums::ChemicalGroupTrapped, the object did not "
352 ✗ "validate successfully.";
353 }
354 3 }
355
356 /*!
357 \brief Returns the polymerization rule.
358 */
359 Enums::ChemicalGroupTrapped
360 2 ChemicalGroup::getPolRule() const
361 {
362 2 return m_polymerizationRule;
363 }
364
365 /*!
366 \brief Returns a const reference to the container of ChemicalGroupRule
367 instances.
368 */
369 const std::vector<ChemicalGroupRuleSPtr> &
370 5 ChemicalGroup::getRulesCstRef() const
371 {
372 5 return m_rules;
373 }
374
375
376 /*!
377 \brief Returns a reference to the container of ChemicalGroupRule instances.
378 */
379 std::vector<ChemicalGroupRuleSPtr> &
380 10 ChemicalGroup::getRulesRef()
381 {
382 10 return m_rules;
383 }
384
385 /*!
386 \brief Searches by \a entity for a ChemicalGroupRule instance.
387
388 Returns the \a index of the ChemicalGroupRule instance in the member list of
389 ChemicalGroupRule instances or -1 if not found.
390 */
391 ChemicalGroupRuleSPtr
392 8 ChemicalGroup::findRuleByEntity(const QString &entity, std::size_t &index) const
393 {
394
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 8 if(index >= m_rules.size())
395 1 return nullptr;
396
397
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 7 if(entity.isEmpty())
398 ✗ return nullptr;
399
400 7 std::vector<ChemicalGroupRuleSPtr>::const_iterator the_begin_iterator_cst =
401 7 m_rules.cbegin();
402 7 std::vector<ChemicalGroupRuleSPtr>::const_iterator the_iterator_cst =
403 7 m_rules.cbegin() + index;
404 7 std::vector<ChemicalGroupRuleSPtr>::const_iterator the_end_iterator_cst =
405 7 m_rules.cend();
406
407
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408 {
409
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 8 if((*the_iterator_cst)->getEntity() == entity)
410 {
411 6 index = std::distance(the_begin_iterator_cst, the_iterator_cst);
412 6 return *the_iterator_cst;
413 }
414
415 2 ++the_iterator_cst;
416 }
417
418 1 return nullptr;
419 }
420
421 /*!
422 \brief Searches by \a name for a ChemicalGroupRule instance.
423
424 Returns the \a index of the ChemicalGroupRule instance in the member list of
425 ChemicalGroupRule instances or -1 if not found.
426 */
427 ChemicalGroupRuleSPtr
428 6 ChemicalGroup::findRuleByName(const QString &name, std::size_t &index) const
429 {
430
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431 1 return nullptr;
432
433
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 5 if(name.isEmpty())
434 ✗ return nullptr;
435
436
437 5 std::vector<ChemicalGroupRuleSPtr>::const_iterator the_begin_iterator_cst =
438 5 m_rules.cbegin();
439 5 std::vector<ChemicalGroupRuleSPtr>::const_iterator the_iterator_cst =
440 5 m_rules.cbegin() + index;
441 5 std::vector<ChemicalGroupRuleSPtr>::const_iterator the_end_iterator_cst =
442 5 m_rules.cend();
443
444
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445 {
446
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 8 if((*the_iterator_cst)->getName() == name)
447 {
448 4 index = std::distance(the_begin_iterator_cst, the_iterator_cst);
449 4 return *the_iterator_cst;
450 }
451
452 4 ++the_iterator_cst;
453 }
454
455 1 return nullptr;
456 }
457
458
459 /*!
460 \brief Searches by \a entity and \a name for a ChemicalGroupRule instance.
461
462 Returns the \a index of the ChemicalGroupRule instance in the member list of
463 ChemicalGroupRule instances or -1 if not found.
464 */
465 ChemicalGroupRuleSPtr
466 4 ChemicalGroup::findRuleByEntityAndName(const QString &entity,
467 const QString &name,
468 std::size_t &index) const
469 {
470
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471 ✗ return nullptr;
472
473
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 4 if(name.isEmpty())
474 ✗ return nullptr;
475
476 4 std::vector<ChemicalGroupRuleSPtr>::const_iterator the_begin_iterator_cst =
477 4 m_rules.cbegin();
478 4 std::vector<ChemicalGroupRuleSPtr>::const_iterator the_iterator_cst =
479 4 m_rules.cbegin() + index;
480 4 std::vector<ChemicalGroupRuleSPtr>::const_iterator the_end_iterator_cst =
481 4 m_rules.cend();
482
483
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484 {
485
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 16 if((*the_iterator_cst)->getName() == name &&
486
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 6 (*the_iterator_cst)->getEntity() == entity)
487 {
488 4 index = std::distance(the_begin_iterator_cst, the_iterator_cst);
489 4 return *the_iterator_cst;
490 }
491
492 2 ++the_iterator_cst;
493 }
494
495 ✗ return nullptr;
496 }
497
498 /*!
499 \brief Validates this instance, setting eventual error messages in \a
500 error_list_p.
501
502 \note \a error_list_p is not cleared.
503
504 If the validation is successful, m_isValid is set to true, otherwise it is set
505 to false. That result is returned.
506 */
507 bool
508 22 ChemicalGroup::validate(ErrorList *error_list_p) const
509 {
510
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 22 qsizetype error_count = error_list_p->size();
511
512
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 22 if(m_name.isEmpty())
513 {
514
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 7 qCritical() << "The ChemicalGroup cannot validate with an empty name.";
515 14 error_list_p->push_back(
516 "The ChemicalGroup cannot validate with an empty name");
517 }
518
519 22 if(m_pka <= 0 && m_pka >= 14)
520 {
521 qCritical()
522 << "The ChemicalGroup cannot validate with an invalid pKa value.";
523 error_list_p->push_back(
524 "The ChemicalGroup cannot validate with an invalid pKa value.");
525 }
526
527 22 m_isValid = error_list_p->size() > error_count ? false : true;
528
529 22 return m_isValid;
530 }
531
532
533 /*!
534 \brief Returns the validity status of this instance.
535 */
536 bool
537 5 ChemicalGroup::isValid() const
538 {
539 5 return m_isValid;
540 }
541
542 /*!
543 \brief Parses the ChemicalGroup XML \a element \e{related to a \l Monomer}.
544
545 Upon parsing of the \a element (tag \code{<mnmchemgroup>}), its data
546 are validated and set to this ChemicalGroup instance, thus essentially
547 initializing it.
548
549 In an pkaphpidata definition file, the following xml structure
550 is encountered:
551
552 \code
553 <pkaphpidata>
554 <monomers>
555 <monomer>
556 <code>A</code>
557 <mnmchemgroup>
558 <name>N-term NH2</name>
559 <pka>9.6</pka>
560 <acidcharged>TRUE</acidcharged>
561 <polrule>left_trapped</polrule>
562 <chemgrouprule>
563 <entity>LE_PLM_MODIF</entity>
564 <name>Acetylation</name>
565 <outcome>LOST</outcome>
566 </chemgrouprule>
567 </mnmchemgroup>
568 <mnmchemgroup>
569 <name>C-term COOH</name>
570 <pka>2.35</pka>
571 <acidcharged>FALSE</acidcharged>
572 <polrule>right_trapped</polrule>
573 </mnmchemgroup>
574 </monomer>
575 <monomer>
576 <code>C</code>
577 <mnmchemgroup>
578 <name>N-term NH2</name>
579 <pka>9.6</pka>
580 <acidcharged>TRUE</acidcharged>
581 <polrule>left_trapped</polrule>
582 <chemgrouprule>
583 <entity>LE_PLM_MODIF</entity>
584 <name>Acetylation</name>
585 <outcome>LOST</outcome>
586 </chemgrouprule>
587 </mnmchemgroup>
588 <mnmchemgroup>
589 <name>C-term COOH</name>
590 <pka>2.35</pka>
591 <acidcharged>FALSE</acidcharged>
592 <polrule>right_trapped</polrule>
593 </mnmchemgroup>
594 <mnmchemgroup>
595 <name>Lateral SH2</name>
596 <pka>8.3</pka>
597 <acidcharged>FALSE</acidcharged>
598 <polrule>never_trapped</polrule>
599 </mnmchemgroup>
600 </monomer>
601 \endcode
602
603 Upon parsing of the \a element, all the data are validated and set to this
604 ChemicalGroup instance, thus essentially initializing it. If there are
605 \l{ChemicalGroupRule}s associated to the ChemicalGroup element, these are
606 rendered also.
607
608 Returns true if parsing and validation were successful, false otherwise.
609 */
610 bool
611 1 ChemicalGroup::renderXmlMnmElement(const QDomElement &element)
612 {
613 // The element the parameter points to is:
614 //
615 // <mnmchemgroup>
616 //
617 // Which means that element.tagName() == "mnmchemgroup" and that we'll
618 // have to go one step down to the first child of the current node
619 // in order to get to the \code<name>\endcode element.
620
621
622 1 QDomElement child;
623
624
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 2 if(element.tagName() != "mnmchemgroup")
625 return false;
626
627
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 2 child = element.firstChildElement("name");
628
629
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 1 if(child.isNull())
630 return false;
631
632
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 1 m_name = child.text();
633
634
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 2 child = child.nextSiblingElement();
635
636
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 2 if(child.isNull() || child.tagName() != "pka")
637 return false;
638
639 1 bool ok = false;
640
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 1 m_pka = child.text().toFloat(&ok);
641
642
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 1 if(!m_pka && !ok)
643 return false;
644
645
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 1 if(m_pka <= 0 || m_pka >= 14)
646 return false;
647
648
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 2 child = child.nextSiblingElement();
649
650
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 2 if(child.isNull() || child.tagName() != "acidcharged")
651 return false;
652
653
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 2 if(child.text() != "FALSE" && child.text() != "TRUE")
654 return false;
655
656
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 3 m_acidCharged = (child.text() == "FALSE" ? false : true);
657
658 // And now the polrule element. There should be one, here, in fact,
659 // because we are dealing with a monomer, and not a modification.
660
661
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 2 child = child.nextSiblingElement();
662
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 2 if(child.isNull() || child.tagName() != "polrule")
664 return false;
665
666
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 2 if(child.text() == "never_trapped")
667 ✗ m_polymerizationRule = Enums::ChemicalGroupTrapped::NEVER;
668
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 2 else if(child.text() == "left_trapped")
669 1 m_polymerizationRule = Enums::ChemicalGroupTrapped::LEFT;
670 ✗ else if(child.text() == "right_trapped")
671 ✗ m_polymerizationRule = Enums::ChemicalGroupTrapped::RIGHT;
672 else
673 return false;
674
675 // And finally the chemical group rules... There might be zero, one
676 // or more.
677
678
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 2 QDomElement childChemGroupRule = child.nextSiblingElement("chemgrouprule");
679
680
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 2 while(!childChemGroupRule.isNull())
681 {
682
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 1 ChemicalGroupRuleSPtr chemical_group_rule_sp =
683 std::make_shared<ChemicalGroupRule>();
684
685
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 1 if(!chemical_group_rule_sp->renderXmlElement(childChemGroupRule))
686 {
687 ✗ chemical_group_rule_sp.reset();
688 ✗ return false;
689 }
690
691
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 1 m_rules.push_back(chemical_group_rule_sp);
692
693
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 2 childChemGroupRule = childChemGroupRule.nextSiblingElement();
694 1 }
695
696 1 ErrorList error_list;
697
698
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 1 m_isValid = validate(&error_list);
699
700
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 1 if(!m_isValid)
701 ✗ qCritical() << "Failed to validate successfully, with errors:" << Utils::joinErrorList(error_list);
702
703 1 return m_isValid;
704 3 }
705
706
707 /*!
708 \brief Parses the ChemicalGroup XML \a element \e{related to a \l Modif}.
709
710 Upon parsing of the \a element (tag <mnmchemgroup>), its data are validated and
711 set to this ChemicalGroup instance, thus essentially initializing it.
712
713 In an pkaphpidata definition file, the following xml structure
714 is encountered:
715
716 \code
717 <pkaphpidata>
718 <monomers>
719 <monomer>
720 <code>A</code>
721 <mnmchemgroup>
722 <name>N-term NH2</name>
723 <pka>9.6</pka>
724 <acidcharged>TRUE</acidcharged>
725 <polrule>left_trapped</polrule>
726 <chemgrouprule>
727 <entity>LE_PLM_MODIF</entity>
728 <name>Acetylation</name>
729 <outcome>LOST</outcome>
730 </chemgrouprule>
731 </mnmchemgroup>
732 <mnmchemgroup>
733 <name>C-term COOH</name>
734 <pka>2.35</pka>
735 <acidcharged>FALSE</acidcharged>
736 <polrule>right_trapped</polrule>
737 </mnmchemgroup>
738 </monomer>
739 .......
740 </monomers>
741 <modifs>
742 <modif>
743 <name>Phosphorylation</name>
744 <mdfchemgroup>
745 <name>none_set</name>
746 <pka>1.2</pka>
747 <acidcharged>FALSE</acidcharged>
748 </mdfchemgroup>
749 <mdfchemgroup>
750 <name>none_set</name>
751 <pka>6.5</pka>
752 <acidcharged>FALSE</acidcharged>
753 </mdfchemgroup>
754 </modif>
755 </modifs>
756 </pkaphpidata>
757 \endcode
758
759 Upon parsing of the \a element, all the data are validated and set to this
760 ChemicalGroup instance, thus essentially initializing it. If there are
761 \l{ChemicalGroupRule}s associated to the ChemicalGroup element, these are
762 rendered also.
763
764 Returns true if parsing and validation were successful, false otherwise.
765 */
766 bool
767 1 ChemicalGroup::renderXmlMdfElement(const QDomElement &element)
768 {
769 1 QDomElement child;
770
771
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 2 if(element.tagName() != "mdfchemgroup")
772 return false;
773
774
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775
776
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777 return false;
778
779
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 1 m_name = child.text();
780
781
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782
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 2 if(child.isNull() || child.tagName() != "pka")
784 return false;
785
786 1 bool ok = false;
787
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 1 m_pka = child.text().toFloat(&ok);
788
789
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790 return false;
791
792
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 1 if(m_pka <= 0 || m_pka >= 14)
793 return false;
794
795
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796
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 2 if(child.isNull() || child.tagName() != "acidcharged")
798 return false;
799
800
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801 return false;
802
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804
805 1 ErrorList error_list;
806
807
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808
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810 ✗ qCritical() << "Failed to validate successfully, with errors:" << Utils::joinErrorList(error_list);
811
812 1 return m_isValid;
813 2 }
814
815
816 //////////////////////// ChemicalGroupProp ////////////////////////
817 //////////////////////// ChemicalGroupProp ////////////////////////
818
819
820 /*!
821 \class MsXpS::libXpertMassCore::ChemicalGroupProp
822 \inmodule libXpertMassCore
823 \ingroup ThePropSystem
824
825 \brief The ChemicalGroupProp class provides a Prop instance of which the member
826 data points to a dynamically allocated \l ChemicalGroup instance.
827 */
828
829 /*!
830 \brief Constructs a ChemicalGroupProp instance using \a data and \a name.
831
832 The \a data pointer is set to the \l mpa_data member.
833 */
834 ✗ ChemicalGroupProp::ChemicalGroupProp(const QString &name, ChemicalGroup *data)
835 {
836 ✗ if(!name.isEmpty())
837 ✗ m_name = name;
838 else
839 ✗ m_name = QString();
840
841 ✗ mpa_data = static_cast<void *>(data);
842 ✗ }
843
844
845 /*!
846 \brief Constructs a ChemicalGroupProp instance as a copy of \a other.
847
848 The data in \a other are duplicated and set to this ChemicalGroupProp instance.
849 */
850 ✗ ChemicalGroupProp::ChemicalGroupProp(const ChemicalGroupProp &other)
851 ✗ : Prop(other)
852 {
853 ✗ if(other.mpa_data != nullptr)
854 {
855 ✗ ChemicalGroup *chemicalGroup =
856 static_cast<ChemicalGroup *>(other.mpa_data);
857
858 ✗ mpa_data = static_cast<void *>(new ChemicalGroup(*chemicalGroup));
859 }
860 else
861 ✗ mpa_data = nullptr;
862 ✗ }
863
864 /*!
865 \brief Destructs this ChemicalGroupProp instance.
866
867 The deletion of the data are delegated to \l deleteData().
868 */
869 ✗ ChemicalGroupProp::~ChemicalGroupProp()
870 {
871 ✗ deleteData();
872 ✗ }
873
874 /*!
875 \brief Deletes the member data.
876 */
877 void
878 ✗ ChemicalGroupProp::deleteData()
879 {
880 ✗ if(mpa_data != nullptr)
881 {
882 ✗ delete static_cast<ChemicalGroup *>(mpa_data);
883 ✗ mpa_data = nullptr;
884 }
885 ✗ }
886
887 /*!
888 \brief Assigns \a other to this ChemicalGroupProp instance.
889
890 The member data are first deleted and then set to a copy of those in \a other.
891 */
892 ChemicalGroupProp &
893 ✗ ChemicalGroupProp::operator=(const ChemicalGroupProp &other)
894 {
895 ✗ if(&other == this)
896 return *this;
897
898 ✗ Prop::operator=(other);
899
900 ✗ if(mpa_data != nullptr)
901 ✗ deleteData();
902
903 ✗ if(other.mpa_data != nullptr)
904 {
905 ✗ ChemicalGroup *chemicalGroup =
906 static_cast<ChemicalGroup *>(other.mpa_data);
907
908 ✗ mpa_data = static_cast<void *>(new ChemicalGroup(*chemicalGroup));
909 }
910 else
911 ✗ mpa_data = nullptr;
912
913 return *this;
914 }
915
916
917 /*!
918 \brief Duplicates this ChemicalGroupProp instance and returns its pointer.
919 */
920 ChemicalGroupProp *
921 ✗ ChemicalGroupProp::cloneOut() const
922 {
923 ✗ ChemicalGroupProp *new_p = new ChemicalGroupProp(*this);
924
925 ✗ return new_p;
926 }
927
928 bool
929 ✗ ChemicalGroupProp::renderXmlElement([[maybe_unused]] const QDomElement &element,
930 [[maybe_unused]] int version)
931 {
932 ✗ return false;
933 }
934
935 QString
936 ✗ ChemicalGroupProp::formatXmlElement([[maybe_unused]] int offset,
937 [[maybe_unused]] const QString &indent)
938 {
939 ✗ return QString();
940 }
941
942 } // namespace libXpertMassCore
943
944 } // namespace MsXpS
945