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 "../../pappsoexception.h"
34#include "../../exception/exceptioninterrupted.h"
35#include "../../processing/filters/filterresample.h"
36
37namespace pappso
38{
39
40
42 : pappso::MsRunXicExtractorInterface(msrun_reader)
43{
44
46 msp_msrun_reader.get()->readSpectrumCollection(get_msrun_points);
47
48 std::sort(m_msrun_points.begin(),
49 m_msrun_points.end(),
50 [](const MsRunXicExtractorPoints &a,
51 const MsRunXicExtractorPoints &b) { return a.rt < b.rt; });
52
53
54 if(m_msrun_points.size() == 0)
55 {
57 QObject::tr("error extracting XIC: no MS level 1 in data file"));
58 }
59}
61{
62}
63
64
67{
69}
70
71
72void
74 UiMonitorInterface &monitor,
75 std::vector<XicCoordSPtr>::iterator it_xic_coord_list_begin,
76 std::vector<XicCoordSPtr>::iterator it_xic_coord_list_end)
77{
78
79 // sort xic by mz:
80 std::sort(it_xic_coord_list_begin,
81 it_xic_coord_list_end,
83 return a.get()->rtTarget < b.get()->rtTarget;
84 });
85
86 for(auto it = it_xic_coord_list_begin; it != it_xic_coord_list_end; it++)
87 {
88 // XicCoord *p_xic_coord = sp_xic_coord.get();
89 extractOneXicCoord(*(it->get()));
90 monitor.count();
91 if(monitor.shouldIstop())
92 {
94 QObject::tr("Xic extraction process interrupted"));
95 }
96 }
97}
98
99
100void
102{
103 FilterResampleKeepXRange keep_range(xic_coord.mzRange.lower(),
104 xic_coord.mzRange.upper());
105 std::shared_ptr<Xic> msrunxic_sp = xic_coord.xicSptr;
106
107 double rt_begin = xic_coord.rtTarget - m_retentionTimeAroundTarget;
108 double rt_end = xic_coord.rtTarget + m_retentionTimeAroundTarget;
109
110
111 auto itpoints = m_msrun_points.begin();
112
113 // find startint retention time :
114 while((itpoints != m_msrun_points.end()) && (itpoints->rt < rt_begin))
115 {
116 itpoints++;
117 }
118 MassSpectrumSPtr spectrum;
119 DataPoint peak;
120 while((itpoints != m_msrun_points.end()) && (itpoints->rt <= rt_end))
121 {
122 spectrum =
123 msp_msrun_reader.get()->massSpectrumSPtr(itpoints->spectrum_index);
124 // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
125 // << spectrum->size(); spectrum->debugPrintValues();
126
127 qDebug() << " spectrum->size()=" << spectrum->size();
128 keep_range.filter(*(spectrum.get()));
129 qDebug() << " spectrum->size()=" << spectrum->size();
130
131 peak.x = itpoints->rt;
132
134 {
135 peak.y = 0;
136 if(spectrum->size() > 0)
137 {
138 peak.y = maxYDataPoint(spectrum->begin(), spectrum->end())->y;
139
140 qDebug() << " peak.y=" << peak.y
141 << " spectrum->size()=" << spectrum->size();
142 }
143 }
144 else
145 {
146 peak.y = sumYTrace(spectrum->begin(), spectrum->end(), 0);
147 }
148 msrunxic_sp->push_back(peak);
149
150 itpoints++;
151 }
152}
153
154void
156 std::vector<Xic *> &xic_list,
157 const std::vector<MzRange> &mass_range_list,
158 pappso::pappso_double rt_begin,
160{
161 qDebug();
162
163 std::vector<DataPoint> peak_for_mass;
164 for(const MzRange &mass_range : mass_range_list)
165 {
166 peak_for_mass.push_back(DataPoint());
167 qDebug() << " mass_range=" << mass_range.getMz();
168 }
169
170
171 qDebug();
172
173 auto itpoints = m_msrun_points.begin();
174
175 while((itpoints != m_msrun_points.end()) && (itpoints->rt < rt_begin))
176 {
177 itpoints++;
178 }
179
180 MassSpectrumCstSPtr spectrum;
181 while((itpoints != m_msrun_points.end()) && (itpoints->rt <= rt_end))
182 {
183 spectrum =
184 msp_msrun_reader.get()->massSpectrumCstSPtr(itpoints->spectrum_index);
185
186 for(DataPoint &peak : peak_for_mass)
187 {
188 peak.x = itpoints->rt;
189 peak.y = 0;
190 }
191
192
193 // iterate through the m/z-intensity pairs
194 for(auto &&spectrum_point : *(spectrum.get()))
195 {
196 // qDebug() << "getXicFromPwizMSDataFile it->mz " << it->mz <<
197 // " it->intensity" << it->intensity;
198 for(std::size_t i = 0; i < mass_range_list.size(); i++)
199 {
200 if(mass_range_list[i].contains(spectrum_point.x))
201 {
203 {
204 if(peak_for_mass[i].y < spectrum_point.y)
205 {
206 peak_for_mass[i].y = spectrum_point.y;
207 }
208 }
209 else
210 {
211 peak_for_mass[i].y += spectrum_point.y;
212 }
213 }
214 }
215 }
216
217 for(std::size_t i = 0; i < mass_range_list.size(); i++)
218 {
219 // qDebug() << "getXicFromPwizMSDataFile push_back " <<
220 // peak_for_mass[i].rt;
221 xic_list[i]->push_back(peak_for_mass[i]);
222 }
223
224 itpoints++;
225 }
226
227
228 qDebug();
229} // namespace pappso
230
231
232} // 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:184
std::vector< DataPoint >::const_iterator maxYDataPoint(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
Definition: trace.cpp:141
double pappso_double
A type definition for doubles.
Definition: types.h:48
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:205
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54
@ max
maximum of intensities
std::shared_ptr< XicCoord > XicCoordSPtr
Definition: xiccoord.h:43
pappso_double x
Definition: datapoint.h:22
pappso_double y
Definition: datapoint.h:23
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