libpappsomspp
Library for mass spectrometry
qualifiedmassspectrum.cpp
Go to the documentation of this file.
1/*******************************************************************************
2 * Copyright (c) 2015 Olivier Langella <olivier.langella@u-psud.fr>.
3 *
4 * This file is part of the PAPPSOms++ library.
5 *
6 * PAPPSOms++ is free software: you can redistribute it and/or modify
7 * it under the terms of the GNU General Public License as published by
8 * the Free Software Foundation, either version 3 of the License, or
9 * (at your option) any later version.
10 *
11 * PAPPSOms++ is distributed in the hope that it will be useful,
12 * but WITHOUT ANY WARRANTY; without even the implied warranty of
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 * GNU General Public License for more details.
15 *
16 * You should have received a copy of the GNU General Public License
17 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
18 *
19 ******************************************************************************/
20
21/////////////////////// StdLib includes
22#include <cmath>
23
24
25/////////////////////// Qt includes
26#include <QDebug>
27
28
29/////////////////////// Local includes
31#include "../utils.h"
32#include "../pappsoexception.h"
33
34
35namespace pappso
36{
37
38//! Construct an uninitialized QualifiedMassSpectrum.
40{
41}
42
43
44//! Construct a QualifiedMassSpectrum using a MassSpectrumId;
46 : m_massSpectrumId(id)
47{
48}
49
50
52 MassSpectrumSPtr mass_spectrum_SPtr)
53 : msp_massSpectrum{mass_spectrum_SPtr}
54{
55}
56
57
58//! Construct a QualifiedMassSpectrum as a copy of \p other.
60 : msp_massSpectrum(other.msp_massSpectrum),
61 m_massSpectrumId(other.m_massSpectrumId),
62 m_isEmptyMassSpectrum(other.m_isEmptyMassSpectrum),
63 m_msLevel(other.m_msLevel),
64 m_rt(other.m_rt),
65 m_dt(other.m_dt),
66 m_precursorSpectrumIndex(other.m_precursorSpectrumIndex),
67 m_precursorNativeId(other.m_precursorNativeId),
68 m_precursorIonData(other.m_precursorIonData),
69 m_paramsMap(other.m_paramsMap)
70{
71 // qDebug();
72}
73
74
75//! Destruct this QualifiedMassSpectrum.
77{
78 // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << " ()";
79}
80
81
84{
88 m_msLevel = other.m_msLevel;
89 m_rt = other.m_rt;
90 m_dt = other.m_dt;
95
96 return *this;
97}
98
99
102{
103 this->msp_massSpectrum =
104 std::make_shared<MassSpectrum>(*this->msp_massSpectrum.get());
105 return *this;
106}
107
108
111{
112 return std::make_shared<QualifiedMassSpectrum>(*this);
113}
114
115
118{
119 return std::make_shared<const QualifiedMassSpectrum>(*this);
120}
121
122
123//! Set the MassSpectrumSPtr.
124void
126{
127 msp_massSpectrum = massSpectrum;
128}
129
130
131//! Get the MassSpectrumSPtr.
134{
135 return msp_massSpectrum;
136}
137
138
139//! Get the MassSpectrumCstSPtr.
142{
143 return msp_massSpectrum;
144}
145
146
147//! Set the MassSpectrumId.
148void
150{
151 m_massSpectrumId = iD;
152}
153
154
155//! Get the MassSpectrumId.
156const MassSpectrumId &
158{
159 return m_massSpectrumId;
160}
161
162
163void
165{
166 m_isEmptyMassSpectrum = is_empty_mass_spectrum;
167}
168
169
170bool
172{
174}
175
176
177//! Set the mass spectrum level.
178void
180{
181 m_msLevel = level;
182}
183
184
185//! Get the mass spectrum level.
186unsigned int
188{
189 return m_msLevel;
190}
191
192
193//! Set the retention time in seconds.
194void
196{
197 m_rt = rt_in_seconds;
198}
199
200
201//! Get the retention time in seconds.
204{
205 return m_rt;
206}
207
208
209//! Get the retention time in minutes.
212{
213 return m_rt / 60;
214}
215
216
217//! Set the drift time in milliseconds.
218void
220{
221 if(std::isinf(dt_in_milli_seconds))
222 m_dt = -1;
223 else
224 m_dt = dt_in_milli_seconds;
225}
226
227
228//! Get the drift time in milliseconds.
231{
232 return m_dt;
233}
234
235
236//! Get the precursor m/z ratio.
239{
240 if(!m_precursorIonData.size())
241 {
242 if(ok_p != nullptr)
243 *ok_p = false;
244
245 return std::numeric_limits<double>::max();
246 }
247
248 if(ok_p != nullptr)
249 *ok_p = true;
250
251 // qDebug() << "Returning precursor mz value: " <<
252 // m_precursorIonData.front().mz;
253 return m_precursorIonData.front().mz;
254}
255
256
257QString
259 const std::vector<PrecursorIonData> &precursor_ion_data_vector,
260 const QString &separator) const
261{
262 QString text;
263
264 // We do not want to use the separator if there is only one precursor in the
265 // vector.
266
267 if(precursor_ion_data_vector.size() == 1)
268 return QString("%1").arg(precursor_ion_data_vector.front().mz, 0, 'f', 6);
269
270 // If there are more than one precursor, then we should list them joined with
271 // the separator.
272
273 using iterator = std::vector<pappso::PrecursorIonData>::const_iterator;
274
275 iterator begin_iterator = precursor_ion_data_vector.begin();
276 iterator pre_end_iterator = std::prev(precursor_ion_data_vector.end());
277
278 for(; begin_iterator != precursor_ion_data_vector.end(); ++begin_iterator)
279 {
280 if(begin_iterator == pre_end_iterator)
281 // No separator at the end of the string
282 text += QString("%1").arg(begin_iterator->mz, 0, 'f', 6);
283 else
284 text +=
285 QString("%1%2").arg(begin_iterator->mz, 0, 'f', 6).arg(separator);
286 }
287
288 return text;
289}
290
291
292QString
294 const QString &separator) const
295{
297}
298
299
300QString
302 const QString &separator) const
303{
304 // Sort the PrecursorIonData instances by increasing mz values.
305 // Then craft the string using the mz values.
306
307 std::vector<PrecursorIonData> sorted_vector =
309
310 return getPrecursorDataMzValuesAsString(sorted_vector, separator);
311}
312
313
314//! Get the precursor charge.
315unsigned int
317{
318 if(!m_precursorIonData.size())
319 {
320 return std::numeric_limits<unsigned int>::max();
321
322 if(ok_p != nullptr)
323 *ok_p = false;
324 }
325
326 if(ok_p != nullptr)
327 *ok_p = true;
328
329 return m_precursorIonData.front().charge;
330}
331
332
333QString
335 const std::vector<PrecursorIonData> &precursor_ion_data_vector,
336 const QString &separator) const
337{
338 QString text;
339
340 // We do not want to use the separator if there is only one precursor in the
341 // vector.
342
343 if(precursor_ion_data_vector.size() == 1)
344 return QString("%1").arg(precursor_ion_data_vector.front().charge);
345
346 // If there are more than one precursor, then we should list them joined with
347 // the separator.
348 for(auto item : precursor_ion_data_vector)
349 {
350 text += QString("%1%2").arg(item.charge).arg(separator);
351 }
352
353 return text;
354}
355
356
357QString
359 const QString &separator) const
360{
362}
363
364
365QString
367 const QString &separator) const
368{
369 // Sort the PrecursorIonData instances by increasing mz values.
370 // Then craft the string using the mz values.
371
372 std::vector<PrecursorIonData> sorted_vector =
374
375 return getPrecursorDataChargeValuesAsString(sorted_vector, separator);
376}
377
378
379//! Get the intensity of the precursor ion.
382{
383 if(!m_precursorIonData.size())
384 {
385 return std::numeric_limits<double>::max();
386
387 if(ok_p != nullptr)
388 *ok_p = false;
389 }
390
391 if(ok_p != nullptr)
392 *ok_p = true;
393
394 return m_precursorIonData.front().intensity;
395}
396
397
398//! Set the scan number of the precursor ion.
399void
401 std::size_t precursor_spectrum_index)
402{
403 m_precursorSpectrumIndex = precursor_spectrum_index;
404}
405
406
407//! Get the scan number of the precursor ion.
408std::size_t
410{
412}
413
414
415//! Set the scan native id of the precursor ion.
416void
418{
419 m_precursorNativeId = native_id;
420}
421
422const QString &
424{
425 return m_precursorNativeId;
426}
427
428
429void
431 const PrecursorIonData &precursor_ion_data)
432{
433 m_precursorIonData.push_back(precursor_ion_data);
434}
435
436
437const std::vector<PrecursorIonData> &
439{
440 return m_precursorIonData;
441}
442
443
444std::vector<PrecursorIonData>
446{
447 std::vector<PrecursorIonData> new_vector;
448 new_vector.assign(m_precursorIonData.begin(), m_precursorIonData.end());
449
450 std::sort(new_vector.begin(),
451 new_vector.end(),
452 [](const PrecursorIonData &a, const PrecursorIonData &b) -> bool {
453 return a.mz < b.mz;
454 });
455
456 return new_vector;
457}
458
459
460void
462 QualifiedMassSpectrumParameter parameter, const QVariant &value)
463{
464
465 auto ret = m_paramsMap.insert(
466 std::pair<QualifiedMassSpectrumParameter, QVariant>(parameter, value));
467
468 if(ret.second == false)
469 {
470 ret.first->second = value;
471 }
472}
473
474
475const QVariant
477 QualifiedMassSpectrumParameter parameter) const
478{
479 auto it = m_paramsMap.find(parameter);
480 if(it == m_paramsMap.end())
481 {
482 return QVariant();
483 }
484 else
485 {
486 return it->second;
487 }
488}
489
490
491std::size_t
493{
494 if(msp_massSpectrum == nullptr)
495 {
496 throw pappso::PappsoException(QObject::tr("msp_massSpectrum == nullptr"));
497 }
498 return msp_massSpectrum.get()->size();
499}
500
501
502QString
504{
505 QString text;
506
507 if(msp_massSpectrum != nullptr && msp_massSpectrum.get() != nullptr)
508 {
509 QString pointer_string =
510 QString("msp_massSpectrum.get(): %1 ")
511 .arg(Utils::pointerToString((void *)msp_massSpectrum.get()));
512
513 text += pointer_string;
514 }
515 else
516 text += QString("msp_massSpectrum is nullptr ");
517
518 // qDebug() << text;
519
520 QString precursor_mz_values_string;
521
522 if(m_precursorIonData.size())
523 precursor_mz_values_string += "Precursor mz values: ";
524
525 precursor_mz_values_string += getMzSortedPrecursorDataMzValuesAsString();
526
527 precursor_mz_values_string += "\n";
528
529 text +=
530 QString(
531 "; m_massSpectrumId : %1 \n"
532 "m_msLevel: %2 ; m_rt (min): %3 ; m_dt (ms): %4 ; prec. spec. "
533 "index: %5 ; %6")
535 .arg(m_msLevel)
536 .arg(getRtInMinutes(), 0, 'f', 2)
537 .arg(m_dt, 0, 'f', 5)
538 .arg(m_precursorSpectrumIndex != std::numeric_limits<std::size_t>::max()
540 : -1)
541 .arg(precursor_mz_values_string);
542
543 if(with_data)
544 {
545 text += msp_massSpectrum->toString();
546 }
547
548 return text;
549}
550
551
552} // namespace pappso
QString toString() const
Class representing a fully specified mass spectrum.
uint getMsLevel() const
Get the mass spectrum level.
QualifiedMassSpectrum & operator=(const QualifiedMassSpectrum &other)
MassSpectrumCstSPtr getMassSpectrumCstSPtr() const
Get the MassSpectrumCstSPtr.
std::vector< PrecursorIonData > m_precursorIonData
std::vector< PrecursorIonData > getPrecursorIonDataSortedWithMz() const
void setPrecursorNativeId(const QString &native_id)
Set the scan native id of the precursor ion.
std::size_t m_precursorSpectrumIndex
Index of the spectrum of the precusor ion that was fragmented to yield.
pappso_double getDtInMilliSeconds() const
Get the drift time in milliseconds.
const std::vector< PrecursorIonData > & getPrecursorIonData() const
uint getPrecursorCharge(bool *ok=nullptr) const
Get the precursor charge.
pappso_double getRtInMinutes() const
Get the retention time in minutes.
unsigned int m_msLevel
Mass spectrometry level of this mass spectrum.
void setDtInMilliSeconds(pappso_double rt)
Set the drift time in milliseconds.
~QualifiedMassSpectrum()
Destruct this QualifiedMassSpectrum.
const QString & getPrecursorNativeId() const
pappso_double m_rt
Retention time (in seconds) at which this mass spectrum was acquired.
pappso_double m_dt
Drift time (in milliseconds) at which this mass spectrum was acquired.
pappso_double getPrecursorIntensity(bool *ok=nullptr) const
Get the intensity of the precursor ion.
QString toString(bool with_data=false) const
void appendPrecursorIonData(const PrecursorIonData &precursor_ion_data)
std::map< QualifiedMassSpectrumParameter, QVariant > m_paramsMap
map containing any parameter value for this spectrum
MassSpectrumSPtr msp_massSpectrum
Shared pointer to the mass spectrum.
const MassSpectrumId & getMassSpectrumId() const
Get the MassSpectrumId.
QString getPrecursorDataChargeValuesAsString(const std::vector< PrecursorIonData > &precursor_ion_data_vector, const QString &separator="\n") const
void setMassSpectrumId(const MassSpectrumId &iD)
Set the MassSpectrumId.
void setMsLevel(uint ms_level)
Set the mass spectrum level.
void setPrecursorSpectrumIndex(std::size_t precursor_scan_num)
Set the scan number of the precursor ion.
QString getPrecursorDataMzValuesAsString(const std::vector< PrecursorIonData > &precursor_ion_data_vector, const QString &separator="\n") const
QualifiedMassSpectrumCstSPtr makeQualifiedMassSpectrumCstSPtr() const
pappso_double getPrecursorMz(bool *ok=nullptr) const
Get the precursor m/z ratio.
const QualifiedMassSpectrum & cloneMassSpectrumSPtr()
clone the mass spectrum contained in Qualified Mass Spectrum
QString getMzSortedPrecursorDataMzValuesAsString(const QString &separator="\n") const
MassSpectrumSPtr getMassSpectrumSPtr() const
Get the MassSpectrumSPtr.
QString getMzSortedPrecursorDataChargeValuesAsString(const QString &separator="\n") const
QString m_precursorNativeId
Native XML id of the spectrum relative to the mz data native file.
QualifiedMassSpectrumSPtr makeQualifiedMassSpectrumSPtr() const
MassSpectrumId m_massSpectrumId
Id of the mass spectrum.
void setParameterValue(QualifiedMassSpectrumParameter parameter, const QVariant &value)
QualifiedMassSpectrum()
Construct an uninitialized QualifiedMassSpectrum.
void setMassSpectrumSPtr(MassSpectrumSPtr massSpectrum)
Set the MassSpectrumSPtr.
std::size_t getPrecursorSpectrumIndex() const
Get the scan number of the precursor ion.
void setRtInSeconds(pappso_double rt)
Set the retention time in seconds.
pappso_double getRtInSeconds() const
Get the retention time in seconds.
void setEmptyMassSpectrum(bool is_empty_mass_spectrum)
const QVariant getParameterValue(QualifiedMassSpectrumParameter parameter) const
static QString pointerToString(const void *const pointer)
Definition: utils.cpp:251
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< QualifiedMassSpectrum > QualifiedMassSpectrumSPtr
double pappso_double
A type definition for doubles.
Definition: types.h:50
std::shared_ptr< const QualifiedMassSpectrum > QualifiedMassSpectrumCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54