pappso::MsRunXicExtractor Class Reference

#include <msrunxicextractor.h>

Inheritance diagram for pappso::MsRunXicExtractor:

Public Member Functions
	MsRunXicExtractor (const MsRunXicExtractor &other)
virtual	~MsRunXicExtractor ()
virtual XicCstSPtr	getXicCstSPtr (const MzRange &mz_range, pappso::pappso_double rt_begin, pappso::pappso_double rt_end) override
	get a XIC on this MsRun at the given mass range More...
virtual std::vector< XicCstSPtr >	getXicCstSPtrList (const std::vector< MzRange > &mz_range_list) override
	extract a list of XIC given a list of mass to extract More...
Public Member Functions inherited from pappso::MsRunXicExtractorInterface
void	setXicExtractMethod (XicExtractMethod method)
	set the XIC extraction method More...
virtual XicCstSPtr	getXicCstSPtr (const MzRange &mz_range) final
	get a XIC on this MsRun at the given mass range More...
const MsRunIdCstSPtr &	getMsRunId () const

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)
Protected Member Functions inherited from pappso::MsRunXicExtractorInterface
	MsRunXicExtractorInterface (MsRunReaderSPtr &msrun_reader)
	constructor is private, use the MsRunXicExtractorFactory More...
	MsRunXicExtractorInterface (const MsRunXicExtractorInterface &other)
virtual	~MsRunXicExtractorInterface ()

Protected Attributes
std::vector< MsRunXicExtractorPoints >	m_msrun_points
Protected Attributes inherited from pappso::MsRunXicExtractorInterface
MsRunReaderSPtr	msp_msrun_reader
XicExtractMethod	m_xicExtractMethod = XicExtractMethod::max

Private Attributes
friend	MsRunXicExtractorFactory

Detailed Description

Definition at line 40 of file msrunxicextractor.h.

Constructor & Destructor Documentation

MsRunXicExtractor() [1/2]

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

protected

Definition at line 59 of file msrunxicextractor.cpp.

{
}
 
 
MsRunXicExtractor::MsRunXicExtractor(const MsRunXicExtractor &other)
  : MsRunXicExtractorInterface(other)
{
  m_msrun_points = other.m_msrun_points;
}
 
XicCstSPtr
MsRunXicExtractor::getXicCstSPtr(const MzRange &mz_range,
                                 pappso::pappso_double rt_begin,
                                 pappso::pappso_double rt_end)
{
  FilterResampleKeepXRange keep_range(mz_range.lower(), mz_range.upper());
  std::shared_ptr<Xic> msrunxic_sp = std::make_shared<Xic>(Xic());
 

MsRunXicExtractor() [2/2]

pappso::MsRunXicExtractor::MsRunXicExtractor

(

const MsRunXicExtractor &

other

)

Definition at line 83 of file msrunxicextractor.cpp.

    {

~MsRunXicExtractor()

pappso::MsRunXicExtractor::~MsRunXicExtractor ( )

virtual

Definition at line 78 of file msrunxicextractor.cpp.

    {

Member Function Documentation

getXicCstSPtr()

XicCstSPtr pappso::MsRunXicExtractor::getXicCstSPtr ( const MzRange &  mz_range, pappso::pappso_double  rt_begin, pappso::pappso_double  rt_end  )

overridevirtual

get a XIC on this MsRun at the given mass range

Parameters

mz_range	mz range to extract
rt_begin	begining of the XIC in seconds
rt_end	end of the XIC in seconds

Implements pappso::MsRunXicExtractorInterface.

Reimplemented in pappso::MsRunXicExtractorDisk.

Definition at line 90 of file msrunxicextractor.cpp.

        {
          peak.y = 0;
          if(spectrum->size() > 0)
            {
              peak.y = maxYDataPoint(spectrum->begin(), spectrum->end())->y;
 
              qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
                       << " peak.y=" << peak.y
                       << " spectrum->size()=" << spectrum->size();
            }
        }
      else
        {
          peak.y = sumYTrace(spectrum->begin(), spectrum->end(), 0);
        }
      msrunxic_sp->push_back(peak);
 
      itpoints++;
    }
 
 
  return (msrunxic_sp);
}
 
std::vector<XicCstSPtr>
MsRunXicExtractor::getXicCstSPtrList(const std::vector<MzRange> &mz_range_list)
{
 
  std::vector<std::shared_ptr<Xic>> xic_list_return;
  std::vector<Xic *> xic_list;
  for(std::size_t i = 0; i < mz_range_list.size(); i++)
    {
      xic_list_return.push_back(std::make_shared<Xic>(Xic()));
      xic_list.push_back(xic_list_return.back().get());
      xic_list_return.back().get()->reserve(m_msrun_points.size());
    }
  getXicFromPwizMSDataFile(xic_list, mz_range_list, 0, 100000000);
  std::vector<XicCstSPtr> xic_list_return_b;
  for(auto &xic : xic_list_return)
    {
      xic_list_return_b.push_back(xic);
    }

References pappso::maxYDataPoint(), pappso::DataPoint::y, and pappso::y.

getXicCstSPtrList()

std::vector< XicCstSPtr > pappso::MsRunXicExtractor::getXicCstSPtrList ( const std::vector< MzRange > &  mz_range_list )

overridevirtual

extract a list of XIC given a list of mass to extract

Implements pappso::MsRunXicExtractorInterface.

Reimplemented in pappso::MsRunXicExtractorDisk.

Definition at line 147 of file msrunxicextractor.cpp.

{
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
 
  std::vector<DataPoint> peak_for_mass;
  for(const MzRange &mass_range : mass_range_list)
    {
      peak_for_mass.push_back(DataPoint());
      qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
               << " mass_range=" << mass_range.getMz();
    }
 
 

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 168 of file msrunxicextractor.cpp.

    {
      itpoints++;
    }
 
  MassSpectrumCstSPtr spectrum;
  while((itpoints != m_msrun_points.end()) && (itpoints->rt <= rt_end))
    {
      spectrum =
        msp_msrun_reader.get()->massSpectrumCstSPtr(itpoints->spectrum_index);
 
      for(DataPoint &peak : peak_for_mass)
        {
          peak.x = itpoints->rt;
          peak.y = 0;
        }
 
 
      // iterate through the m/z-intensity pairs
      for(auto &&spectrum_point : *(spectrum.get()))
        {
          // qDebug() << "getXicFromPwizMSDataFile it->mz " << it->mz <<
          // " it->intensity" << it->intensity;
          for(std::size_t i = 0; i < mass_range_list.size(); i++)
            {
              if(mass_range_list[i].contains(spectrum_point.x))
                {
                  if(m_xicExtractMethod == XicExtractMethod::max)
                    {
                      if(peak_for_mass[i].y < spectrum_point.y)
                        {
                          peak_for_mass[i].y = spectrum_point.y;
                        }
                    }
                  else
                    {
                      peak_for_mass[i].y += spectrum_point.y;
                    }
                }
            }
        }
 
      for(std::size_t i = 0; i < mass_range_list.size(); i++)
        {
          // qDebug() << "getXicFromPwizMSDataFile push_back " <<
          // peak_for_mass[i].rt;
          xic_list[i]->push_back(peak_for_mass[i]);
        }
 
      itpoints++;
    }
 
 
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
} // namespace pappso
 
 
} // namespace pappso

Member Data Documentation

m_msrun_points

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

protected

Definition at line 45 of file msrunxicextractor.h.

MsRunXicExtractorFactory

friend pappso::MsRunXicExtractor::MsRunXicExtractorFactory

private

Definition at line 42 of file msrunxicextractor.h.

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

• pappsomspp/xicextractor/private/msrunxicextractor.h
• pappsomspp/xicextractor/private/msrunxicextractor.cpp