#include <msrunxicextractor.h>
Definition at line 41 of file msrunxicextractor.h.
◆ MsRunXicExtractor() [1/2]
◆ ~MsRunXicExtractor()
pappso::MsRunXicExtractor::~MsRunXicExtractor |
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◆ MsRunXicExtractor() [2/2]
pappso::MsRunXicExtractor::MsRunXicExtractor |
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MsRunReaderSPtr & |
msrun_reader | ) |
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◆ extractOneXicCoord()
void pappso::MsRunXicExtractor::extractOneXicCoord |
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XicCoord & |
xic_coord | ) |
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Definition at line 103 of file msrunxicextractor.cpp.
105 FilterResampleKeepXRange keep_range(xic_coord.mzRange.lower(),
106 xic_coord.mzRange.upper());
107 std::shared_ptr<Xic> msrunxic_sp = xic_coord.xicSptr;
116 while((itpoints !=
m_msrun_points.end()) && (itpoints->rt < rt_begin))
122 while((itpoints !=
m_msrun_points.end()) && (itpoints->rt <= rt_end))
129 qDebug() <<
" spectrum->size()=" << spectrum->size();
130 keep_range.filter(*(spectrum.get()));
131 qDebug() <<
" spectrum->size()=" << spectrum->size();
133 peak.x = itpoints->rt;
138 if(spectrum->size() > 0)
140 peak.y =
maxYDataPoint(spectrum->begin(), spectrum->end())->y;
142 qDebug() <<
" peak.y=" << peak.y
143 <<
" spectrum->size()=" << spectrum->size();
148 peak.y =
sumYTrace(spectrum->begin(), spectrum->end(), 0);
150 msrunxic_sp->push_back(peak);
std::vector< DataPoint >::const_iterator maxYDataPoint(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
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
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()
Definition at line 157 of file msrunxicextractor.cpp.
165 std::vector<DataPoint> peak_for_mass;
166 for(
const MzRange &mass_range : mass_range_list)
168 peak_for_mass.push_back(DataPoint());
169 qDebug() <<
" mass_range=" << mass_range.getMz();
177 while((itpoints !=
m_msrun_points.end()) && (itpoints->rt < rt_begin))
183 while((itpoints !=
m_msrun_points.end()) && (itpoints->rt <= rt_end))
188 for(DataPoint &peak : peak_for_mass)
190 peak.x = itpoints->rt;
196 for(
auto &&spectrum_point : *(spectrum.get()))
200 for(std::size_t i = 0; i < mass_range_list.size(); i++)
202 if(mass_range_list[i].contains(spectrum_point.x))
206 if(peak_for_mass[i].y < spectrum_point.y)
208 peak_for_mass[i].y = spectrum_point.y;
213 peak_for_mass[i].y += spectrum_point.y;
219 for(std::size_t i = 0; i < mass_range_list.size(); i++)
223 xic_list[i]->push_back(peak_for_mass[i]);
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 |
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UiMonitorInterface & |
monitor, |
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std::vector< XicCoordSPtr >::iterator |
it_xic_coord_list_begin, |
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std::vector< XicCoordSPtr >::iterator |
it_xic_coord_list_end |
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◆ m_msrun_points
◆ MsRunXicExtractorFactory
friend pappso::MsRunXicExtractor::MsRunXicExtractorFactory |
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private |
The documentation for this class was generated from the following files: