libpappsomspp
Library for mass spectrometry
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pappso::MsRunXicExtractor Class Reference

#include <msrunxicextractor.h>

Inheritance diagram for pappso::MsRunXicExtractor:
pappso::MsRunXicExtractorInterface pappso::MsRunXicExtractorDisk pappso::MsRunXicExtractorDiskBuffer

Classes

struct  MsRunXicExtractorPoints
 
class  MsRunXicExtractorReadPoints
 class to read retention time points of MsRun More...
 

Public Member Functions

 MsRunXicExtractor (const MsRunXicExtractor &other)
 
virtual ~MsRunXicExtractor ()
 
- Public Member Functions inherited from pappso::MsRunXicExtractorInterface
void setXicExtractMethod (XicExtractMethod method)
 set the XIC extraction method
 
void setRetentionTimeAroundTarget (double range_in_seconds)
 set the retention time range in seconds around the target rt
 
virtual void extractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr > &xic_coord_list) final
 extract a list of XIC given a list of xic coordinates to extract
 
virtual void extractXicCoordSPtrListParallelized (UiMonitorInterface &monitor, std::vector< XicCoordSPtr > &xic_coord_list) final
 multithreaded XIC extraction
 
const MsRunIdCstSPtrgetMsRunId () const
 
const MsRunReaderSPtrgetMsRunReaderSPtr () const
 get the msrunreader currently used for XIC extraction
 
void setPostExtractionTraceFilterCstSPtr (pappso::FilterInterfaceCstSPtr &filter)
 filter interface to apply just after XIC extration on each trace
 

Protected Member Functions

 MsRunXicExtractor (MsRunReaderSPtr &msrun_reader)
 
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)
 
virtual void protectedExtractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end) override
 
- Protected Member Functions inherited from pappso::MsRunXicExtractorInterface
 MsRunXicExtractorInterface (MsRunReaderSPtr &msrun_reader)
 constructor is private, use the MsRunXicExtractorFactory
 
 MsRunXicExtractorInterface (const MsRunXicExtractorInterface &other)
 
virtual ~MsRunXicExtractorInterface ()
 
virtual void postExtractionProcess (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end)
 possible post extraction process, eventually trace filters
 

Protected Attributes

std::vector< MsRunXicExtractorPointsm_msrun_points
 
- Protected Attributes inherited from pappso::MsRunXicExtractorInterface
MsRunReaderSPtr msp_msrun_reader
 
XicExtractMethod m_xicExtractMethod = XicExtractMethod::max
 
double m_retentionTimeAroundTarget = std::numeric_limits<double>::max()
 
pappso::FilterInterfaceCstSPtr mcsp_postExtractionTraceFilter = nullptr
 

Private Member Functions

void extractOneXicCoord (XicCoord &xic_coord)
 

Private Attributes

friend MsRunXicExtractorFactory
 

Detailed Description

Definition at line 41 of file msrunxicextractor.h.

Constructor & Destructor Documentation

◆ MsRunXicExtractor() [1/2]

pappso::MsRunXicExtractor::MsRunXicExtractor ( const MsRunXicExtractor & other)

Definition at line 67 of file msrunxicextractor.cpp.

69{
70 m_msrun_points = other.m_msrun_points;
71}
MsRunXicExtractorInterface(MsRunReaderSPtr &msrun_reader)
constructor is private, use the MsRunXicExtractorFactory
std::vector< MsRunXicExtractorPoints > m_msrun_points

References m_msrun_points.

◆ ~MsRunXicExtractor()

pappso::MsRunXicExtractor::~MsRunXicExtractor ( )
virtual

Definition at line 62 of file msrunxicextractor.cpp.

63{
64}

◆ MsRunXicExtractor() [2/2]

pappso::MsRunXicExtractor::MsRunXicExtractor ( MsRunReaderSPtr & msrun_reader)
protected

Definition at line 43 of file msrunxicextractor.cpp.

45{
46
47 MsRunXicExtractorReadPoints get_msrun_points(m_msrun_points);
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}

References pappso::a, pappso::b, m_msrun_points, and pappso::MsRunXicExtractorInterface::msp_msrun_reader.

Member Function Documentation

◆ extractOneXicCoord()

void pappso::MsRunXicExtractor::extractOneXicCoord ( XicCoord & xic_coord)
private

Definition at line 103 of file msrunxicextractor.cpp.

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}
std::vector< DataPoint >::const_iterator maxYDataPoint(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
Definition trace.cpp:180
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
@ max
maximum of intensities

References pappso::FilterResampleKeepXRange::filter(), pappso::MzRange::lower(), m_msrun_points, pappso::MsRunXicExtractorInterface::m_retentionTimeAroundTarget, pappso::MsRunXicExtractorInterface::m_xicExtractMethod, pappso::max, pappso::maxYDataPoint(), pappso::MsRunXicExtractorInterface::msp_msrun_reader, pappso::XicCoord::mzRange, pappso::XicCoord::rtTarget, pappso::sumYTrace(), pappso::MzRange::upper(), pappso::DataPoint::x, pappso::XicCoord::xicSptr, and pappso::DataPoint::y.

Referenced by protectedExtractXicCoordSPtrList().

◆ getXicFromPwizMSDataFile()

void pappso::MsRunXicExtractor::getXicFromPwizMSDataFile ( std::vector< Xic * > & xic_list,
const std::vector< MzRange > & mass_range_list,
pappso::pappso_double rt_begin,
pappso::pappso_double rt_end )
protectedvirtual

Definition at line 157 of file msrunxicextractor.cpp.

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
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr

References m_msrun_points, pappso::MsRunXicExtractorInterface::m_xicExtractMethod, pappso::max, pappso::MsRunXicExtractorInterface::msp_msrun_reader, and pappso::y.

◆ protectedExtractXicCoordSPtrList()

void pappso::MsRunXicExtractor::protectedExtractXicCoordSPtrList ( UiMonitorInterface & monitor,
std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin,
std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end )
overrideprotectedvirtual

Implements pappso::MsRunXicExtractorInterface.

Reimplemented in pappso::MsRunXicExtractorDisk.

Definition at line 75 of file msrunxicextractor.cpp.

79{
80
81 // sort xic by mz:
82 std::sort(it_xic_coord_list_begin,
83 it_xic_coord_list_end,
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}
void extractOneXicCoord(XicCoord &xic_coord)
std::shared_ptr< XicCoord > XicCoordSPtr
Definition xiccoord.h:43

References pappso::a, pappso::b, pappso::UiMonitorInterface::count(), extractOneXicCoord(), and pappso::UiMonitorInterface::shouldIstop().

Member Data Documentation

◆ m_msrun_points

std::vector<MsRunXicExtractorPoints> pappso::MsRunXicExtractor::m_msrun_points
protected

◆ MsRunXicExtractorFactory

friend pappso::MsRunXicExtractor::MsRunXicExtractorFactory
private

Definition at line 43 of file msrunxicextractor.h.


The documentation for this class was generated from the following files: