calculate a TIC chromatogram More...

#include <spectrumcollectionhandlerinterface.h>

Inheritance diagram for pappso::MsRunReaderTicChromatogram:

Public Member Functions
	MsRunReaderTicChromatogram ()

virtual	~MsRunReaderTicChromatogram ()

virtual void	setQualifiedMassSpectrum (const QualifiedMassSpectrum &qualified_mass_spectrum) override

virtual bool	needPeakList () const override
	tells if we need the peak list (if we want the binary data) for each spectrum

Trace	getTicChromatogram () const

Public Member Functions inherited from pappso::SpectrumCollectionHandlerInterface
virtual bool	needMsLevelPeakList (unsigned int ms_level) const final
	tells if we need the peak list (if we want the binary data) for each spectrum, given an MS level

virtual void	setNeedMsLevelPeakList (unsigned int ms_level, bool want_peak_list) final
	tells if we need the peak list given

virtual bool	shouldStop ()

virtual void	loadingEnded ()

virtual void	spectrumListHasSize (std::size_t size)

virtual void	setReadAhead (bool is_read_ahead) final
	use threads to read a spectrum by batch of batch_size

virtual bool	isReadAhead () const
	tells if we want to read ahead spectrum

Private Attributes
MapTrace	m_ticChromMapTrace

Detailed Description

calculate a TIC chromatogram

Definition at line 167 of file spectrumcollectionhandlerinterface.h.

Constructor & Destructor Documentation

◆ MsRunReaderTicChromatogram()

pappso::MsRunReaderTicChromatogram::MsRunReaderTicChromatogram ( )

Definition at line 251 of file spectrumcollectionhandlerinterface.cpp.

252{

253}

◆ ~MsRunReaderTicChromatogram()

pappso::MsRunReaderTicChromatogram::~MsRunReaderTicChromatogram ( )

virtual

Definition at line 256 of file spectrumcollectionhandlerinterface.cpp.

257{

258}

Member Function Documentation

◆ getTicChromatogram()

Trace pappso::MsRunReaderTicChromatogram::getTicChromatogram ( ) const

Definition at line 305 of file spectrumcollectionhandlerinterface.cpp.

{
  return m_ticChromMapTrace.toTrace();
}

References m_ticChromMapTrace.

Referenced by pappso::MsRunReader::getTicChromatogram().

◆ needPeakList()

bool pappso::MsRunReaderTicChromatogram::needPeakList ( ) const

overridevirtual

tells if we need the peak list (if we want the binary data) for each spectrum

Implements pappso::SpectrumCollectionHandlerInterface.

Definition at line 262 of file spectrumcollectionhandlerinterface.cpp.

{
  return true;
}

◆ setQualifiedMassSpectrum()

void pappso::MsRunReaderTicChromatogram::setQualifiedMassSpectrum ( const QualifiedMassSpectrum & qualified_mass_spectrum )

overridevirtual

Implements pappso::SpectrumCollectionHandlerInterface.

Definition at line 269 of file spectrumcollectionhandlerinterface.cpp.

{
  // In this specialized reader we want to compute the total ion current
  // chromatogram that plot the sum of all the ion intensities in the spectra as
  // a function of the retention time.
 
  uint spectrum_ms_level = qualified_mass_spectrum.getMsLevel();
 
  if(spectrum_ms_level != 1)
    return;
 
  double sumY = qualified_mass_spectrum.getMassSpectrumSPtr()->sumY();
 
  if(!sumY)
    return;
 
  double rt = qualified_mass_spectrum.getRtInMinutes();
 
  using Pair     = std::pair<double, double>;
  using Map      = std::map<double, double>;
  using Iterator = Map::iterator;
 
  std::pair<Iterator, bool> res = m_ticChromMapTrace.insert(Pair(rt, sumY));
 
  if(!res.second)
    {
      // One other same rt value was seen already (like in ion mobility mass
      // spectrometry, for example). Only increment the y value.
 
      res.first->second += sumY;
    }
}