libpappsomspp
Library for mass spectrometry
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#include <peakpickerqtof.hpp>
Public Types | |
typedef TReal | value_type |
typedef TIntegrator< value_type > | PeakIntegrator |
Public Member Functions | |
PeakPicker (TReal resolution, std::pair< TReal, TReal > &massrange, TReal width=2., TReal intwidth=2., TReal intensitythreshold=10., bool area=true, uint32_t maxnumberofpeaks=0, double c2d=1e-5) | |
template<typename Tmass , typename Tintensity > | |
void | operator() (Tmass begmz, Tmass endmz, Tintensity begint) |
TReal | getNToppeaks () |
get min instensity of peak to qualify for max-intensity; More... | |
void | filter (TReal threshold) |
clean the masses using the threshold More... | |
const std::vector< TReal > & | getPeakMass () |
const std::vector< TReal > & | getPeakArea () |
const std::vector< TReal > & | getResampledMZ () |
const std::vector< TReal > & | getResampledIntensity () |
const std::vector< TReal > & | getSmoothedIntensity () |
Public Attributes | |
TReal | resolution_ |
ralab::base::resample::Convert2Dense | c2d_ |
std::vector< TReal > | resampledmz_ |
std::vector< TReal > | resampledintensity_ |
std::vector< TReal > | filter_ |
std::vector< TReal > | zerocross_ |
std::vector< TReal > | smoothedintensity_ |
std::vector< TReal > | peakmass_ |
std::vector< TReal > | peakarea_ |
TReal | smoothwith_ |
TReal | integrationWidth_ |
ralab::base::ms::SimplePicker< TReal > | simplepicker_ |
ralab::base::resample::SamplingWith | sw_ |
PeakIntegrator | integrator_ |
TReal | intensitythreshold_ |
bool | area_ |
uint32_t | maxnumbersofpeaks_ |
resamples spectrum, apply smoothing, determines zero crossings, integrates peaks.
Definition at line 159 of file peakpickerqtof.hpp.
typedef TIntegrator<value_type> ralab::base::ms::PeakPicker< TReal, TIntegrator >::PeakIntegrator |
Definition at line 161 of file peakpickerqtof.hpp.
typedef TReal ralab::base::ms::PeakPicker< TReal, TIntegrator >::value_type |
Definition at line 160 of file peakpickerqtof.hpp.
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resolution | instrument resolution |
massrange | mass range of spectrum |
width | smooth width |
intwidth | integration width used for area compuation |
area | compute area or height? default - height. |
maxnumberofpeaks | maximum of peaks returned by picker |
c2d | instrument resampling with small default dissables automatic determination |
Definition at line 177 of file peakpickerqtof.hpp.
References ralab::base::ms::PeakPicker< TReal, TIntegrator >::c2d_, ralab::base::resample::Convert2Dense::defBreak(), ralab::base::ms::PeakPicker< TReal, TIntegrator >::filter_, ralab::base::resample::Convert2Dense::getMids(), and ralab::base::ms::PeakPicker< TReal, TIntegrator >::resampledmz_.
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clean the masses using the threshold
Definition at line 261 of file peakpickerqtof.hpp.
References ralab::base::ms::PeakPicker< TReal, TIntegrator >::peakarea_, and ralab::base::ms::PeakPicker< TReal, TIntegrator >::peakmass_.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()().
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get min instensity of peak to qualify for max-intensity;
Definition at line 248 of file peakpickerqtof.hpp.
References ralab::base::ms::PeakPicker< TReal, TIntegrator >::maxnumbersofpeaks_, and ralab::base::ms::PeakPicker< TReal, TIntegrator >::peakarea_.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()().
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Definition at line 275 of file peakpickerqtof.hpp.
References ralab::base::ms::PeakPicker< TReal, TIntegrator >::peakarea_.
Referenced by pappso::FilterPseudoCentroid::filter().
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Definition at line 271 of file peakpickerqtof.hpp.
References ralab::base::ms::PeakPicker< TReal, TIntegrator >::peakmass_.
Referenced by pappso::FilterPseudoCentroid::filter().
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Definition at line 283 of file peakpickerqtof.hpp.
References ralab::base::ms::PeakPicker< TReal, TIntegrator >::resampledintensity_.
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Definition at line 279 of file peakpickerqtof.hpp.
References ralab::base::ms::PeakPicker< TReal, TIntegrator >::resampledmz_.
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Definition at line 287 of file peakpickerqtof.hpp.
References ralab::base::ms::PeakPicker< TReal, TIntegrator >::smoothedintensity_.
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Definition at line 196 of file peakpickerqtof.hpp.
References ralab::base::resample::Convert2Dense::am_, ralab::base::ms::PeakPicker< TReal, TIntegrator >::area_, ralab::base::ms::PeakPicker< TReal, TIntegrator >::c2d_, ralab::base::resample::Convert2Dense::convert2dense(), ralab::base::ms::PeakPicker< TReal, TIntegrator >::filter(), ralab::base::ms::PeakPicker< TReal, TIntegrator >::filter_, ralab::base::ms::PeakPicker< TReal, TIntegrator >::getNToppeaks(), ralab::base::ms::PeakPicker< TReal, TIntegrator >::integrator_, ralab::base::ms::PeakPicker< TReal, TIntegrator >::intensitythreshold_, ralab::base::ms::PeakPicker< TReal, TIntegrator >::maxnumbersofpeaks_, ralab::base::ms::PeakPicker< TReal, TIntegrator >::peakarea_, ralab::base::ms::PeakPicker< TReal, TIntegrator >::peakmass_, ralab::base::ms::PeakPicker< TReal, TIntegrator >::resampledintensity_, ralab::base::ms::PeakPicker< TReal, TIntegrator >::resampledmz_, ralab::base::ms::PeakPicker< TReal, TIntegrator >::simplepicker_, ralab::base::ms::PeakPicker< TReal, TIntegrator >::smoothedintensity_, ralab::base::ms::PeakPicker< TReal, TIntegrator >::sw_, and ralab::base::ms::PeakPicker< TReal, TIntegrator >::zerocross_.
bool ralab::base::ms::PeakPicker< TReal, TIntegrator >::area_ |
Definition at line 174 of file peakpickerqtof.hpp.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()().
ralab::base::resample::Convert2Dense ralab::base::ms::PeakPicker< TReal, TIntegrator >::c2d_ |
Definition at line 164 of file peakpickerqtof.hpp.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()(), and ralab::base::ms::PeakPicker< TReal, TIntegrator >::PeakPicker().
std::vector<TReal> ralab::base::ms::PeakPicker< TReal, TIntegrator >::filter_ |
Definition at line 166 of file peakpickerqtof.hpp.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()(), and ralab::base::ms::PeakPicker< TReal, TIntegrator >::PeakPicker().
TReal ralab::base::ms::PeakPicker< TReal, TIntegrator >::integrationWidth_ |
Definition at line 169 of file peakpickerqtof.hpp.
PeakIntegrator ralab::base::ms::PeakPicker< TReal, TIntegrator >::integrator_ |
Definition at line 172 of file peakpickerqtof.hpp.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()().
TReal ralab::base::ms::PeakPicker< TReal, TIntegrator >::intensitythreshold_ |
Definition at line 173 of file peakpickerqtof.hpp.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()().
uint32_t ralab::base::ms::PeakPicker< TReal, TIntegrator >::maxnumbersofpeaks_ |
Definition at line 175 of file peakpickerqtof.hpp.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::getNToppeaks(), and ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()().
std::vector<TReal> ralab::base::ms::PeakPicker< TReal, TIntegrator >::peakarea_ |
Definition at line 167 of file peakpickerqtof.hpp.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::filter(), ralab::base::ms::PeakPicker< TReal, TIntegrator >::getNToppeaks(), ralab::base::ms::PeakPicker< TReal, TIntegrator >::getPeakArea(), and ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()().
std::vector<TReal> ralab::base::ms::PeakPicker< TReal, TIntegrator >::peakmass_ |
Definition at line 167 of file peakpickerqtof.hpp.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::filter(), ralab::base::ms::PeakPicker< TReal, TIntegrator >::getPeakMass(), and ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()().
std::vector<TReal> ralab::base::ms::PeakPicker< TReal, TIntegrator >::resampledintensity_ |
Definition at line 165 of file peakpickerqtof.hpp.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::getResampledIntensity(), and ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()().
std::vector<TReal> ralab::base::ms::PeakPicker< TReal, TIntegrator >::resampledmz_ |
TReal ralab::base::ms::PeakPicker< TReal, TIntegrator >::resolution_ |
Definition at line 163 of file peakpickerqtof.hpp.
ralab::base::ms::SimplePicker<TReal> ralab::base::ms::PeakPicker< TReal, TIntegrator >::simplepicker_ |
Definition at line 170 of file peakpickerqtof.hpp.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()().
std::vector<TReal> ralab::base::ms::PeakPicker< TReal, TIntegrator >::smoothedintensity_ |
Definition at line 166 of file peakpickerqtof.hpp.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::getSmoothedIntensity(), and ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()().
TReal ralab::base::ms::PeakPicker< TReal, TIntegrator >::smoothwith_ |
Definition at line 168 of file peakpickerqtof.hpp.
ralab::base::resample::SamplingWith ralab::base::ms::PeakPicker< TReal, TIntegrator >::sw_ |
Definition at line 171 of file peakpickerqtof.hpp.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()().
std::vector<TReal> ralab::base::ms::PeakPicker< TReal, TIntegrator >::zerocross_ |
Definition at line 166 of file peakpickerqtof.hpp.
Referenced by ralab::base::ms::PeakPicker< TReal, TIntegrator >::operator()().