libpappsomspp
Library for mass spectrometry
massspectrumwidget.cpp
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1 /**
2  * \file pappsomspp/widget/spectrumwidget/massspectrumwidget.cpp
3  * \date 22/12/2017
4  * \author Olivier Langella
5  * \brief plot a sectrum and annotate with peptide
6  */
7 
8 
9 /*******************************************************************************
10  * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
11  *
12  * This file is part of the PAPPSOms++ library.
13  *
14  * PAPPSOms++ is free software: you can redistribute it and/or modify
15  * it under the terms of the GNU General Public License as published by
16  * the Free Software Foundation, either version 3 of the License, or
17  * (at your option) any later version.
18  *
19  * PAPPSOms++ is distributed in the hope that it will be useful,
20  * but WITHOUT ANY WARRANTY; without even the implied warranty of
21  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22  * GNU General Public License for more details.
23  *
24  * You should have received a copy of the GNU General Public License
25  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
26  *
27  * Contributors:
28  * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
29  *implementation
30  ******************************************************************************/
31 #include "massspectrumwidget.h"
32 #include "../../pappsoexception.h"
33 #include "../../peptide/peptidenaturalisotopelist.h"
34 #include <QDebug>
35 #include <QWidget>
36 
37 
38 using namespace pappso;
39 
41  : GraphicDeviceWidget(parent)
42 {
43  qDebug();
44 
45  _ms_level = 1;
47  _custom_plot = nullptr;
48 
49  this->setLayout(new QHBoxLayout(this));
50 
51  this->layout()->setMargin(0);
52  setVisibleMassDelta(false);
53  qDebug();
54 }
56 {
57 }
58 
59 bool
60 MassSpectrumWidget::savePdf(const QString &fileName, int width, int height)
61 {
62 
63  if(_custom_plot != nullptr)
64  {
65  return _custom_plot->savePdf(fileName, width, height);
66  }
67  else
68  {
69  return false;
70  }
71 }
72 
73 
74 void
75 MassSpectrumWidget::toQPaintDevice(QPaintDevice *device, const QSize &size)
76 {
77 
78  if(_custom_plot != nullptr)
79  {
80  QCPPainter painter;
81  painter.begin(device);
82  _custom_plot->toPainter(&painter, size.width(), size.height());
83  painter.end();
84  }
85 }
86 void
88 {
89  qDebug();
90  if(_custom_plot != nullptr)
91  {
92  if(visible == _is_visible_mass_delta)
93  return;
94  delete _custom_plot;
95  }
96  _is_visible_mass_delta = visible;
97  while(auto item = this->layout()->takeAt(0))
98  {
99  delete item->widget();
100  }
101  qDebug();
102  _custom_plot = new QCPSpectrum(this, visible);
103  this->layout()->addWidget(_custom_plot);
104  qDebug();
105  _custom_plot->xAxis->setLabel("m/z");
106  _custom_plot->yAxis->setLabel("intensity");
107  qDebug();
108  _custom_plot->setInteractions(QCP::iRangeDrag | QCP::iRangeZoom);
109  _custom_plot->axisRect()->setRangeDrag(Qt::Horizontal);
110  _custom_plot->axisRect()->setRangeZoom(Qt::Horizontal);
111  qDebug();
112  // legend->setVisible(false);
113  // legend->setFont(QFont("Helvetica",9));
114  // set locale to english, so we get english decimal separator:
115  // setLocale(QLocale(QLocale::English, QLocale::UnitedKingdom));
116  qDebug();
117 }
118 void
120 {
121  qDebug();
123  qDebug();
124  _custom_plot->clearItems();
126  qDebug();
127 }
128 
129 void
130 MassSpectrumWidget::setPeptideCharge(unsigned int parent_ion_charge)
131 {
132  _peptide_charge = parent_ion_charge;
133 }
134 void
135 MassSpectrumWidget::setIonList(const std::list<PeptideIon> &ion_list)
136 {
137  _ion_list = ion_list;
138 }
139 
140 void
141 MassSpectrumWidget::setMsLevel(unsigned int ms_level)
142 {
143  qDebug() << "ms_level=" << ms_level;
144  _ms_level = ms_level;
145 
146 
147  if(_ms_level == 1)
148  {
149  setVisibleMassDelta(false);
150  }
151  else
152  {
153  setVisibleMassDelta(true);
154  }
155 
156  //_precision._precision = precision._precision;
157 }
158 void
160 {
161  qDebug() << "precision->toString()=" << precision->toString();
162  _p_ms1_precision = precision;
163  //_precision._precision = precision._precision;
164 }
165 void
167 {
168  qDebug() << "precision->toString()=" << precision->toString();
169  _p_ms2_precision = precision;
170  //_precision._precision = precision._precision;
171 }
172 
173 void
174 MassSpectrumWidget::setMaximumIsotopeNumber(unsigned int max_isotope_number)
175 {
176  _max_isotope_number = max_isotope_number;
177 }
178 
179 void
180 MassSpectrumWidget::setMaximumIsotopeRank(unsigned int max_isotope_rank)
181 {
182  _max_isotope_rank = max_isotope_rank;
183 }
184 void
186 {
187  qDebug() << " _max_isotope_number=" << _max_isotope_number;
188  clearData();
190  if((_spectrum_sp == nullptr) || (_peptide_sp == nullptr))
191  {
192  }
193  else
194  {
195  if(_ms_level > 1)
196  {
197  PeptideIsotopeSpectrumMatch psm_match(*(_spectrum_sp.get()),
198  _peptide_sp,
201  _ion_list,
204 
206  }
207  else
208  {
209  }
211  }
212  qDebug();
213 }
214 
215 void
217 {
218  qDebug();
219  _peptide_sp = peptide_sp;
220 
221  // clearData();
222  qDebug();
223 }
224 
225 void
227 {
228  qDebug();
229  _spectrum_sp = spectrum;
230 
231  clearData();
232  qDebug();
233 }
234 
235 void
237 {
238  qDebug();
239 
241 
242  /*
243  if (_p_delta_axis_rect != nullptr) {
244  _p_delta_axis_rect->axis(QCPAxis::AxisType::atLeft)->rescale();
245  }
246  */
247  _custom_plot->replot();
248  qDebug();
249 }
250 
251 void
253  const QualifiedMassSpectrum &spectrum)
254 {
255  qDebug() << "spectrum.getPrecursorCharge()=" << spectrum.getPrecursorCharge();
256 
257  setMsLevel(spectrum.getMsLevel());
259 
260  qDebug();
261 }
262 
263 void
265 {
266 
267  qDebug();
268  peptideAnnotate();
269  if(_ms_level == 1)
270  {
271  if(_spectrum_sp != nullptr)
272  {
273  if(_isotope_mass_list.size() > 0)
274  {
275 
276  qDebug() << "_isotope_mass_list.size()="
277  << _isotope_mass_list.size();
278  std::sort(_isotope_mass_list.begin(),
279  _isotope_mass_list.end(),
280  [](const PeptideNaturalIsotopeAverageSp &a,
282  return a.get()->getMz() < b.get()->getMz();
283  });
284 
285  if(_isotope_mass_list.size() > 0)
286  {
287  PeptideNaturalIsotopeAverageSp precursor_peptide =
288  _isotope_mass_list.at(0);
289  qDebug() << "precursor_peptide.get()->getMz()="
290  << precursor_peptide.get()->getMz();
291  MzRange precursor_mass(precursor_peptide.get()->getMz(),
293  DataPoint monoisotope_peak;
294  monoisotope_peak.y = 0;
295 
296  for(const DataPoint &peak : *(_spectrum_sp.get()))
297  {
298  if(precursor_mass.contains(peak.x))
299  {
300  if(peak.y > monoisotope_peak.y)
301  {
302  qDebug() << "SpectrumWidget::plot "
303  "(peak.intensity > "
304  "monoisotope_peak.intensity) ";
305  monoisotope_peak = peak;
306  }
307  }
308  }
309  if(monoisotope_peak.y > 0)
310  {
311  qDebug() << "addMs1IsotopePattern";
313  monoisotope_peak.y);
314  }
315  }
316  }
317  }
318  }
319  else
320  {
321 
323  [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
324  return a.getPeak().y > b.getPeak().y;
325  });
326  unsigned int i = 0;
327  for(const PeakIonIsotopeMatch &peak_ion_match :
329  {
330  _custom_plot->addPeakIonIsotopeMatch(peak_ion_match);
331 
332  _custom_plot->addMassDelta(peak_ion_match);
333  //_p_delta_graph->addData(peak_ion_match.getPeak().x,
334  // peak_ion_match.getPeak().y);
335  if(i < _tag_nmost_intense)
336  {
337  QString plusstr = "+";
338  plusstr = plusstr.repeated(peak_ion_match.getCharge());
339  QCPItemText *text_label = new QCPItemText(_custom_plot);
340  text_label->setVisible(true);
341  //_custom_plot->addItem(text_label);
342  text_label->setPositionAlignment(Qt::AlignBottom |
343  Qt::AlignHCenter);
344  text_label->position->setType(QCPItemPosition::ptPlotCoords);
345  text_label->position->setCoords(
346  peak_ion_match.getPeak().x,
347  peak_ion_match.getPeak()
348  .y); // place position at center/top of axis rect
349  text_label->setFont(QFont(font().family(), 8));
350  text_label->setText(
351  QString("%1%2%3")
352  .arg(peak_ion_match.getPeptideFragmentIonSp()
353  .get()
354  ->getPeptideIonName())
355  .arg(peak_ion_match.getPeptideFragmentIonSp().get()->size())
356  .arg(plusstr));
357  // text_label->setPen(QPen(PeptideFragmentIon::getPeptideIonColor(peak_ion_match.getPeptideIonType()),
358  // 1)); // show black border around text
359  text_label->setColor(
361  peak_ion_match.getPeptideIonType())));
362  }
363  i++;
364  }
365  }
366 
367  _custom_plot->replot();
368  qDebug();
369 }
370 void
372 {
373  emit mzChanged(mz);
374 }
375 
376 void
378 {
379  qDebug() << "p_peak_match=" << p_peak_match;
380  if(_p_mouse_peak != p_peak_match)
381  {
382  _p_mouse_peak = p_peak_match;
383  DataPointCstSPtr peak_shp;
384  // emit peakChanged(peak_shp);
385  if(_p_mouse_peak != nullptr)
386  {
387  qDebug() << "_p_mouse_peak->x=" << _p_mouse_peak->x;
388  peak_shp = _p_mouse_peak->makeDataPointCstSPtr();
389  emit peakChanged(peak_shp);
390  // try to find matched ion (if it exists)
391  bool found = false;
392  for(const PeakIonIsotopeMatch &peak_ion_match :
394  {
395  if(peak_ion_match.getPeak().x == _p_mouse_peak->x)
396  {
397  // found
398  emit ionChanged(std::make_shared<const PeakIonIsotopeMatch>(
399  PeakIonIsotopeMatch(peak_ion_match)));
400  found = true;
401  }
402  }
403  if(!found)
404  {
405  emit ionChanged(std::shared_ptr<const PeakIonIsotopeMatch>());
406  }
407  }
408  else
409  {
410  qDebug() << "no peak";
411  emit peakChanged(peak_shp);
412  }
413  }
414 }
415 
416 void
418 {
419  qDebug() << "_p_ms1_precision->toString()=" << _p_ms1_precision->toString();
420  _isotope_mass_list.resize(0);
421  // compute isotope masses :
422  if(_peptide_sp != nullptr)
423  {
425  std::map<unsigned int, pappso::pappso_double> map_isotope_number =
426  isotope_list.getIntensityRatioPerIsotopeNumber();
427 
428  for(unsigned int i = 0; i < map_isotope_number.size(); i++)
429  {
430 
431  unsigned int asked_rank = 0;
432  unsigned int given_rank = 0;
433  bool more_rank = true;
434  while(more_rank)
435  {
436  asked_rank++;
437  pappso::PeptideNaturalIsotopeAverage isotopeAverageMono(
438  isotope_list, asked_rank, i, _peptide_charge, _p_ms1_precision);
439  given_rank = isotopeAverageMono.getIsotopeRank();
440  if(given_rank < asked_rank)
441  {
442  more_rank = false;
443  }
444  else if(isotopeAverageMono.getIntensityRatio() == 0)
445  {
446  more_rank = false;
447  }
448  else
449  {
450  // isotopeAverageMono.makePeptideNaturalIsotopeAverageSp();
451  _isotope_mass_list.push_back(
452  isotopeAverageMono.makePeptideNaturalIsotopeAverageSp());
453  }
454  }
455  }
456  }
457 }
pappso::QualifiedMassSpectrum::getMsLevel
uint getMsLevel() const
Get the mass spectrum level.
Definition: qualifiedmassspectrum.cpp:187
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition: types.h:48
pappso::QCPSpectrum::setSpectrumP
void setSpectrumP(const MassSpectrum *spectrum)
Definition: qcpspectrum.cpp:153
pappso::MassSpectrumCstSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55
massspectrumwidget.h
pappso::MassSpectrumWidget::mzChangeEvent
void mzChangeEvent(pappso_double mz) const
Definition: massspectrumwidget.cpp:371
pappso::PeptideIsotopeSpectrumMatch
Definition: peptideisotopespectrummatch.h:40
pappso::MassSpectrumWidget::~MassSpectrumWidget
~MassSpectrumWidget()
Definition: massspectrumwidget.cpp:55
pappso::MassSpectrumWidget::ionChanged
void ionChanged(pappso::PeakIonIsotopeMatchCstSPtr ion) const
pappso::DataPoint::y
pappso_double y
Definition: datapoint.h:23
pappso::PeptideNaturalIsotopeList::getIntensityRatioPerIsotopeNumber
const std::map< unsigned int, pappso_double > getIntensityRatioPerIsotopeNumber() const
Definition: peptidenaturalisotopelist.cpp:293
pappso::MassSpectrumWidget::_isotope_mass_list
std::vector< pappso::PeptideNaturalIsotopeAverageSp > _isotope_mass_list
list of isotope precursors
Definition: massspectrumwidget.h:107
pappso::MassSpectrumWidget::plot
void plot()
Definition: massspectrumwidget.cpp:264
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
pappso::QCPSpectrum::clearData
void clearData()
Definition: qcpspectrum.cpp:238
pappso::MassSpectrumWidget::QCPSpectrum
friend class QCPSpectrum
Definition: massspectrumwidget.h:81
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bool _is_visible_mass_delta
Definition: massspectrumwidget.h:110
pappso::PeptideNaturalIsotopeAverage
Definition: peptidenaturalisotopeaverage.h:43
pappso::MzRange::contains
bool contains(pappso_double) const
Definition: mzrange.cpp:102
pappso::MassSpectrumWidget::setVisibleMassDelta
void setVisibleMassDelta(bool visible)
Definition: massspectrumwidget.cpp:87
pappso::PeakIonMatch::getPeak
const DataPoint & getPeak() const
Definition: peakionmatch.h:55
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unsigned int _max_isotope_number
Definition: massspectrumwidget.h:93
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Definition: datapoint.h:21
pappso::PeptideNaturalIsotopeAverage::getIntensityRatio
pappso_double getIntensityRatio() const
Definition: peptidenaturalisotopeaverage.cpp:184
pappso::MassSpectrumWidget::MassSpectrumWidget
MassSpectrumWidget(QWidget *parent=0)
Definition: massspectrumwidget.cpp:40
pappso::MassSpectrumWidget::setMs1Precision
void setMs1Precision(PrecisionPtr precision)
Definition: massspectrumwidget.cpp:159
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DataPointCstSPtr makeDataPointCstSPtr() const
Definition: datapoint.cpp:70
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void setIonList(const std::list< PeptideIon > &ion_list)
Definition: massspectrumwidget.cpp:135
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void toQPaintDevice(QPaintDevice *device, const QSize &size) override
Definition: massspectrumwidget.cpp:75
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std::shared_ptr< const DataPoint > DataPointCstSPtr
Definition: datapoint.h:16
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void setPeptideSp(const PeptideSp &peptide_sp)
Definition: massspectrumwidget.cpp:216
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Definition: mzrange.h:46
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Definition: massspectrumwidget.h:101
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Definition: massspectrumwidget.cpp:236
pappso::QualifiedMassSpectrum
Class representing a fully specified mass spectrum.
Definition: qualifiedmassspectrum.h:85
pappso::QualifiedMassSpectrum::getPrecursorCharge
uint getPrecursorCharge(bool *ok=nullptr) const
Get the precursor charge.
Definition: qualifiedmassspectrum.cpp:316
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void clearData()
Definition: massspectrumwidget.cpp:119
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Definition: massspectrumwidget.cpp:226
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const std::list< PeakIonIsotopeMatch > & getPeakIonIsotopeMatchList() const
Definition: peptideisotopespectrummatch.cpp:195
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void addMs1IsotopePattern(const std::vector< pappso::PeptideNaturalIsotopeAverageSp > &isotope_mass_list, pappso_double intensity)
Definition: qcpspectrum.cpp:447
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Definition: graphicdevicewidget.h:37
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Definition: massspectrumwidget.h:98
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Definition: massspectrumwidget.cpp:130
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Definition: massspectrumwidget.cpp:252
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Definition: datapoint.h:22
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Definition: massspectrumwidget.h:96
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unsigned int getIsotopeRank() const
Definition: peptidenaturalisotopeaverage.cpp:202
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Definition: massspectrumwidget.cpp:377
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Definition: massspectrumwidget.cpp:180
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Definition: massspectrumwidget.h:99
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Definition: precision.h:44
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Definition: peptidenaturalisotopeaverage.cpp:154
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Definition: peptidefragmention.cpp:173
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Get the MassSpectrumCstSPtr.
Definition: qualifiedmassspectrum.cpp:141
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Definition: massspectrumwidget.cpp:417
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Definition: qcpspectrum.cpp:440
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Definition: massspectrumwidget.h:95
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Definition: massspectrumwidget.h:92
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Definition: massspectrumwidget.h:109
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Definition: massspectrumwidget.cpp:185
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Definition: peptidefragmentionlistbase.cpp:41
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Definition: qcpspectrum.cpp:419
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Definition: peakionisotopematch.h:37
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Definition: massspectrumwidget.cpp:166
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Definition: massspectrumwidget.h:112
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Definition: massspectrumwidget.cpp:141
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Definition: massspectrumwidget.h:100
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Definition: massspectrumwidget.cpp:174
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Definition: aamodification.h:47
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Definition: qcpspectrum.cpp:184
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Definition: massspectrumwidget.h:103
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Definition: massspectrumwidget.h:97
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Definition: peptidenaturalisotopeaverage.h:37
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Definition: peptidenaturalisotopelist.h:49
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Definition: massspectrumwidget.cpp:60
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Definition: massspectrumwidget.h:94