GCC Code Coverage Report

source/XpertMassCore/src/
File: source/XpertMassCore/src/CleavageConfig.cpp
Date: 2025-11-19 15:26:11
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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/CleavageConfig.hpp"
36
37 namespace MsXpS
38 {
39 namespace libXpertMassCore
40 {
41
42
43 /*!
44 \class MsXpS::libXpertMassCore::CleavageConfig
45 \inmodule libXpertMassCore
46 \ingroup PolChemDefAqueousChemicalReactions
47 \inheaderfile CleavageConfig.hpp
48
49 \brief The CleavageConfig class derives from CleavageAgent to provide a model
50 for specifying aqueous cleavage specifications (patterns) of \l{Polymer}
51 \l{Sequence}s along with instructions on the way the cleavage must occur.
52
53 Cleavage agent specifications determine the specificity of cleavage in a polymer
54 sequence using a simple syntax. For example, Trypsin is able to cleave after
55 lysyl and arginyl residues. Its cleavage pattern is thus "Lys/;Arg/". However,
56 it is known that Trypsin fails to cleave after Lys if that monomer is followed
57 by a Prolyl residue, thus the complete cleavage agent pattern specification for
58 Trypsin is the following: "Lys/;Arg/;-Lys/Pro".
59
60 A cleavage agent specification might not be enough information to determine the
61 manner in which a polymer is cleaved. Cleavage rules might be required to refine
62 the specification. A cleavage agent specification might hold as many cleavage
63 rules as required.
64
65 \sa CleavageMotif, CleavageRule
66 */
67
68
69 /*!
70 \variable MsXpS::libXpertMassCore::CleavageConfig::m_partials
71
72 \brief The partial cleavages accepted.
73 */
74
75 /*!
76 \variable MsXpS::libXpertMassCore::CleavageConfig::m_startIonizeLevel
77
78 \brief The first ionization level of the range.
79 */
80
81 /*!
82 \variable MsXpS::libXpertMassCore::CleavageConfig::m_stopIonizeLevel
83
84 \brief The last ionization level of the range.
85 */
86
87
88 /*!
89 \variable MsXpS::libXpertMassCore::CleavageConfig::m_sequenceEmbedded
90
91 \brief Tells if the sequence of the obtained Oligomer instance need to embed
92 their sequence.
93 */
94
95
96 /*!
97 \brief Constructs an empty CleavageConfig instance.
98 */
99 6 CleavageConfig::CleavageConfig(QObject *parent): CleavageAgent(parent)
100 {
101 6 }
102
103 /*!
104 \brief Constructs a CleavageConfig instance using a full set of parameters.
105
106 \list
107 \a pol_chem_def_csp: the polymer chemistry definition.
108
109 \a name: the name of CleavageAgent;
110
111 \a pattern: the cleavage pattern of the CleavageAgent;
112
113 \a partials: the partial cleavages;
114
115 \a is_sequence_embedded: indicates if the Oligomer sequence needs to be stored.
116 \endlist
117 */
118 72 CleavageConfig::CleavageConfig(PolChemDefCstSPtr pol_chem_def_csp,
119 const QString &name,
120 const QString &pattern,
121 int partials,
122 bool is_sequence_embedded,
123 72 QObject *parent)
124 : CleavageAgent(pol_chem_def_csp, name, pattern, parent),
125 72 m_partials(partials),
126
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 72 m_sequenceEmbedded(is_sequence_embedded)
127 {
128 72 }
129
130 /*!
131 \brief Constructs a CleavageConfig instance starting using a limited set of
132 parameters.
133
134 \list
135 \a cleavage_agent: CleavageAgent to be used to initialize the base class.
136
137 \a partials: the partial cleavages;
138
139 \a is_sequence_embedded: indicates if the Oligomer sequence needs to be stored.
140 \endlist
141 */
142 6 CleavageConfig::CleavageConfig(const CleavageAgent &cleavage_agent,
143 int partials,
144 bool is_sequence_embedded,
145 6 QObject *parent)
146 : CleavageAgent(cleavage_agent, parent),
147 6 m_partials(partials),
148 6 m_sequenceEmbedded(is_sequence_embedded)
149 {
150 6 }
151
152 /*!
153 \brief Constructs a CleavageConfig instance as a copy of \a other
154 */
155 66 CleavageConfig::CleavageConfig(const CleavageConfig &other, QObject *parent)
156 : CleavageAgent(other, parent),
157 66 m_partials(other.m_partials),
158 66 m_startIonizeLevel(other.m_startIonizeLevel),
159 66 m_stopIonizeLevel(other.m_stopIonizeLevel),
160 66 m_sequenceEmbedded(other.m_sequenceEmbedded)
161 {
162 66 }
163
164 /*!
165 \brief Destructs this CleavageConfig instance.
166 */
167 300 CleavageConfig::~CleavageConfig()
168 {
169 300 }
170
171 /*!
172 \brief Initializes this CleavageConfig instance using \a other.
173
174 If no initialization error occurred, return true, false otherwise.
175 */
176 bool
177 3 CleavageConfig::initialize(const CleavageConfig &other)
178 {
179 // That call fatal-fails, no need to check bool return value.
180 3 bool ok = CleavageAgent::initialize(other);
181
182
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 3 if(!ok)
183 ✗ qCritical() << "Failed to initalize the CleavageConfig instance.";
184
185 3 m_partials = other.m_partials;
186 3 m_startIonizeLevel = other.m_startIonizeLevel;
187 3 m_stopIonizeLevel = other.m_stopIonizeLevel;
188 3 m_sequenceEmbedded = other.m_sequenceEmbedded;
189
190 3 return ok;
191 }
192
193 /*!
194 \brief Sets this instance's CleavageAgent base class to \a cleavage_agent.
195
196 Returns true the CleavageAgent initialization succeeded, false otherwise.
197 */
198 bool
199 3 CleavageConfig::setCleavageAgent(const CleavageAgent &cleavage_agent)
200 {
201 3 bool ok = CleavageAgent::initialize(cleavage_agent);
202
203
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 3 if(!ok)
204 ✗ qCritical() << "Failed to initalize the CleavageConfig instance.";
205
206 3 return ok;
207 }
208
209 /*!
210 \brief Set the partial cleavages to \a value.
211 */
212 void
213 21 CleavageConfig::setPartials(int value)
214 {
215 21 Q_ASSERT(value >= 0);
216
217 21 m_partials = value;
218 21 }
219
220 /*!
221 \brief Returns the partial cleavages.
222 */
223 int
224 120 CleavageConfig::getPartials() const
225 {
226 120 return m_partials;
227 }
228
229 /*!
230 \brief Sets the ionization start level to \a value.
231 */
232 void
233 24 CleavageConfig::setStartIonizeLevel(int value)
234 {
235 24 int local = (value < 0) ? abs(value) : value;
236
237
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 24 if(local <= m_stopIonizeLevel)
238 {
239 24 m_startIonizeLevel = local;
240 }
241 else
242 {
243 ✗ m_startIonizeLevel = m_stopIonizeLevel;
244 ✗ m_stopIonizeLevel = local;
245 }
246 24 }
247
248 /*!
249 \brief Returns the ionization start level.
250 */
251 int
252 1317 CleavageConfig::getStartIonizeLevel() const
253 {
254 1317 return m_startIonizeLevel;
255 }
256
257 /*!
258 \brief Sets the ionization stop level to \a value.
259 */
260 void
261 24 CleavageConfig::setStopIonizeLevel(int value)
262 {
263 24 int local = (value < 0) ? abs(value) : value;
264
265
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 24 if(local > m_startIonizeLevel)
266 {
267 24 m_stopIonizeLevel = local;
268 }
269 else
270 {
271 ✗ m_startIonizeLevel = m_stopIonizeLevel;
272 ✗ m_stopIonizeLevel = local;
273 }
274 24 }
275
276 /*!
277 \brief Returns the ionization stop level.
278 */
279 int
280 1317 CleavageConfig::getStopIonizeLevel() const
281 {
282 1317 return m_stopIonizeLevel;
283 }
284
285 /*!
286 \brief Sets both the ionization start and stop levels to \a value1 and \a
287 value2, respectively.
288 */
289 void
290 57 CleavageConfig::setIonizeLevels(int value1, int value2)
291 {
292
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 57 if(abs(value1) <= abs(value2))
293 {
294 57 m_startIonizeLevel = abs(value1);
295 57 m_stopIonizeLevel = abs(value2);
296 }
297 else
298 {
299 ✗ m_startIonizeLevel = abs(value2);
300 ✗ m_stopIonizeLevel = abs(value1);
301 }
302 57 }
303
304 /*!
305 \brief Sets the sequence embedded boolean value to \a is_sequence_embedded.
306 */
307 void
308 54 CleavageConfig::setSequenceEmbedded(bool is_sequence_embedded)
309 {
310 54 m_sequenceEmbedded = is_sequence_embedded;
311 54 }
312
313 /*!
314 \brief Returns the sequence embedded boolean value.
315 */
316 bool
317 24 CleavageConfig::isSequenceEmbedded() const
318 {
319 24 return m_sequenceEmbedded;
320 }
321
322 //////////////// OPERATORS /////////////////////
323
324 /*!
325 \brief Returns true if this CleavageConfig instance and \a other are identical, false otherwise.
326 \sa operator!=()
327 */
328 bool
329 15 CleavageConfig::operator==(const CleavageConfig &other) const
330 {
331
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 15 if(&other == this)
332 return true;
333
334
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 30 if(CleavageAgent::operator!=(other) || m_partials != other.m_partials ||
335
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 15 m_startIonizeLevel != other.m_startIonizeLevel ||
336
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 15 m_stopIonizeLevel != other.m_stopIonizeLevel ||
337
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 15 m_sequenceEmbedded != other.m_sequenceEmbedded)
338 return false;
339
340 return true;
341 }
342
343 /*!
344 \brief Returns true if this instance and \a other differ, false otherwise.
345 Returns the negative value of opearator==().
346 \sa operator==()
347 */
348 bool
349 9 CleavageConfig::operator!=(const CleavageConfig &other) const
350 {
351 9 return !operator==(other);
352 }
353
354 void
355 ✗ CleavageConfig::registerJsConstructor(QJSEngine *engine)
356 {
357 ✗ if(!engine)
358 {
359 ✗ qWarning() << "Cannot register CleavageConfig class: engine is null";
360 ✗ return;
361 }
362
363 // Register the meta object as a constructor
364
365 ✗ QJSValue jsMetaObject =
366 ✗ engine->newQMetaObject(&CleavageConfig::staticMetaObject);
367 ✗ engine->globalObject().setProperty("CleavageConfig", jsMetaObject);
368 ✗ }
369
370
371 } // namespace libXpertMassCore
372 } // namespace MsXpS
373