libpappsomspp
Library for mass spectrometry
msrunxicextractor.cpp
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1 /**
2  * \file pappsomspp/xicextractor/private/msrunxicextractorpwiz.cpp
3  * \date 07/05/2018
4  * \author Olivier Langella
5  * \brief simple proteowizard based XIC extractor
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2018 Olivier Langella <Olivier.Langella@u-psud.fr>.
10  *
11  * This file is part of the PAPPSOms++ library.
12  *
13  * PAPPSOms++ is free software: you can redistribute it and/or modify
14  * it under the terms of the GNU General Public License as published by
15  * the Free Software Foundation, either version 3 of the License, or
16  * (at your option) any later version.
17  *
18  * PAPPSOms++ is distributed in the hope that it will be useful,
19  * but WITHOUT ANY WARRANTY; without even the implied warranty of
20  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21  * GNU General Public License for more details.
22  *
23  * You should have received a copy of the GNU General Public License
24  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25  *
26  * Contributors:
27  * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
28  *implementation
29  ******************************************************************************/
30 
31 #include "msrunxicextractor.h"
32 #include <QDebug>
33 #include <QObject>
34 
35 #include "../../pappsoexception.h"
36 #include "../../exception/exceptioninterrupted.h"
37 #include "../../processing/filters/filterresample.h"
38 
39 namespace pappso
40 {
41 
42 
44  : pappso::MsRunXicExtractorInterface(msrun_reader)
45 {
46 
48  msp_msrun_reader.get()->readSpectrumCollection(get_msrun_points);
49 
50  std::sort(m_msrun_points.begin(),
51  m_msrun_points.end(),
52  [](const MsRunXicExtractorPoints &a,
53  const MsRunXicExtractorPoints &b) { return a.rt < b.rt; });
54 
55 
56  if(m_msrun_points.size() == 0)
57  {
59  QObject::tr("error extracting XIC: no MS level 1 in data file"));
60  }
61 }
63 {
64 }
65 
66 
69 {
71 }
72 
73 
74 void
76  UiMonitorInterface &monitor,
77  std::vector<XicCoordSPtr>::iterator it_xic_coord_list_begin,
78  std::vector<XicCoordSPtr>::iterator it_xic_coord_list_end)
79 {
80 
81  // sort xic by mz:
82  std::sort(it_xic_coord_list_begin,
83  it_xic_coord_list_end,
84  [](XicCoordSPtr &a, XicCoordSPtr &b) {
85  return a.get()->rtTarget < b.get()->rtTarget;
86  });
87 
88  for(auto it = it_xic_coord_list_begin; it != it_xic_coord_list_end; it++)
89  {
90  // XicCoord *p_xic_coord = sp_xic_coord.get();
91  extractOneXicCoord(*(it->get()));
92  monitor.count();
93  if(monitor.shouldIstop())
94  {
96  QObject::tr("Xic extraction process interrupted"));
97  }
98  }
99 }
100 
101 
102 void
104 {
105  FilterResampleKeepXRange keep_range(xic_coord.mzRange.lower(),
106  xic_coord.mzRange.upper());
107  std::shared_ptr<Xic> msrunxic_sp = xic_coord.xicSptr;
108 
109  double rt_begin = xic_coord.rtTarget - m_retentionTimeAroundTarget;
110  double rt_end = xic_coord.rtTarget + m_retentionTimeAroundTarget;
111 
112 
113  auto itpoints = m_msrun_points.begin();
114 
115  // find startint retention time :
116  while((itpoints != m_msrun_points.end()) && (itpoints->rt < rt_begin))
117  {
118  itpoints++;
119  }
120  MassSpectrumSPtr spectrum;
121  DataPoint peak;
122  while((itpoints != m_msrun_points.end()) && (itpoints->rt <= rt_end))
123  {
124  spectrum =
125  msp_msrun_reader.get()->massSpectrumSPtr(itpoints->spectrum_index);
126  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
127  // << spectrum->size(); spectrum->debugPrintValues();
128 
129  qDebug() << " spectrum->size()=" << spectrum->size();
130  keep_range.filter(*(spectrum.get()));
131  qDebug() << " spectrum->size()=" << spectrum->size();
132 
133  peak.x = itpoints->rt;
134 
136  {
137  peak.y = 0;
138  if(spectrum->size() > 0)
139  {
140  peak.y = maxYDataPoint(spectrum->begin(), spectrum->end())->y;
141 
142  qDebug() << " peak.y=" << peak.y
143  << " spectrum->size()=" << spectrum->size();
144  }
145  }
146  else
147  {
148  peak.y = sumYTrace(spectrum->begin(), spectrum->end(), 0);
149  }
150  msrunxic_sp->push_back(peak);
151 
152  itpoints++;
153  }
154 }
155 
156 void
158  std::vector<Xic *> &xic_list,
159  const std::vector<MzRange> &mass_range_list,
160  pappso::pappso_double rt_begin,
161  pappso::pappso_double rt_end)
162 {
163  qDebug();
164 
165  std::vector<DataPoint> peak_for_mass;
166  for(const MzRange &mass_range : mass_range_list)
167  {
168  peak_for_mass.push_back(DataPoint());
169  qDebug() << " mass_range=" << mass_range.getMz();
170  }
171 
172 
173  qDebug();
174 
175  auto itpoints = m_msrun_points.begin();
176 
177  while((itpoints != m_msrun_points.end()) && (itpoints->rt < rt_begin))
178  {
179  itpoints++;
180  }
181 
182  MassSpectrumCstSPtr spectrum;
183  while((itpoints != m_msrun_points.end()) && (itpoints->rt <= rt_end))
184  {
185  spectrum =
186  msp_msrun_reader.get()->massSpectrumCstSPtr(itpoints->spectrum_index);
187 
188  for(DataPoint &peak : peak_for_mass)
189  {
190  peak.x = itpoints->rt;
191  peak.y = 0;
192  }
193 
194 
195  // iterate through the m/z-intensity pairs
196  for(auto &&spectrum_point : *(spectrum.get()))
197  {
198  // qDebug() << "getXicFromPwizMSDataFile it->mz " << it->mz <<
199  // " it->intensity" << it->intensity;
200  for(std::size_t i = 0; i < mass_range_list.size(); i++)
201  {
202  if(mass_range_list[i].contains(spectrum_point.x))
203  {
205  {
206  if(peak_for_mass[i].y < spectrum_point.y)
207  {
208  peak_for_mass[i].y = spectrum_point.y;
209  }
210  }
211  else
212  {
213  peak_for_mass[i].y += spectrum_point.y;
214  }
215  }
216  }
217  }
218 
219  for(std::size_t i = 0; i < mass_range_list.size(); i++)
220  {
221  // qDebug() << "getXicFromPwizMSDataFile push_back " <<
222  // peak_for_mass[i].rt;
223  xic_list[i]->push_back(peak_for_mass[i]);
224  }
225 
226  itpoints++;
227  }
228 
229 
230  qDebug();
231 } // namespace pappso
232 
233 
234 } // namespace pappso
Trace & filter(Trace &trace) const override
class to read retention time points of MsRun
virtual void getXicFromPwizMSDataFile(std::vector< Xic * > &xic_list, const std::vector< MzRange > &mass_range_list, pappso::pappso_double rt_begin, pappso::pappso_double rt_end)
MsRunXicExtractor(const MsRunXicExtractor &other)
void extractOneXicCoord(XicCoord &xic_coord)
std::vector< MsRunXicExtractorPoints > m_msrun_points
virtual void protectedExtractXicCoordSPtrList(UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end) override
pappso_double lower() const
Definition: mzrange.h:71
pappso_double upper() const
Definition: mzrange.h:77
virtual bool shouldIstop()=0
should the procces be stopped ? If true, then cancel process Use this function at strategic point of ...
virtual void count()=0
count steps report when a step is computed in an algorithm
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< MsRunReader > MsRunReaderSPtr
Definition: msrunreader.h:185
std::vector< DataPoint >::const_iterator maxYDataPoint(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
Definition: trace.cpp:180
double pappso_double
A type definition for doubles.
Definition: types.h:49
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55
double sumYTrace(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double init)
calculate the sum of y value of a trace
Definition: trace.cpp:244
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54
@ max
maximum of intensities
std::shared_ptr< XicCoord > XicCoordSPtr
Definition: xiccoord.h:41
pappso_double x
Definition: datapoint.h:23
pappso_double y
Definition: datapoint.h:24
coordinates of the XIC to extract and the resulting XIC after extraction
Definition: xiccoord.h:54
XicSPtr xicSptr
extracted xic
Definition: xiccoord.h:113
double rtTarget
the targeted retention time to extract around intended in seconds, and related to one msrun....
Definition: xiccoord.h:109
MzRange mzRange
the mass to extract
Definition: xiccoord.h:103