pappso::cbor::mzcbor::QcborSpectrumPrecursor Class Reference

#include <qcborspectrumprecursor.h>

Inheritance diagram for pappso::cbor::mzcbor::QcborSpectrumPrecursor:

Public Member Functions
	QcborSpectrumPrecursor (const QCborMap &cbor_map)
	QcborSpectrumPrecursor (const QcborSpectrumPrecursor &other)
QString	getSpectrumRef () const
void	setSpectrumRef (const QString &spectrum_ref)
std::vector< SelectedIon >	getSelectedIonList () const
IsolationWindow	getIsolationWindow () const
void	setSelectedIon (double mz, double intensity, int charge)

Detailed Description

Todo

write docs

Definition at line 46 of file qcborspectrumprecursor.h.

Constructor & Destructor Documentation

QcborSpectrumPrecursor() [1/2]

pappso::cbor::mzcbor::QcborSpectrumPrecursor::QcborSpectrumPrecursor

(

const QCborMap &

cbor_map

)

Definition at line 44 of file qcborspectrumprecursor.cpp.

                                                                       : QCborMap(cbor_map)
{
}

Referenced by QcborSpectrumPrecursor().

QcborSpectrumPrecursor() [2/2]

pappso::cbor::mzcbor::QcborSpectrumPrecursor::QcborSpectrumPrecursor

(

const QcborSpectrumPrecursor &

other

)

Definition at line 47 of file qcborspectrumprecursor.cpp.

  : QCborMap(other)
{
}

References QcborSpectrumPrecursor().

Member Function Documentation

getIsolationWindow()

IsolationWindow pappso::cbor::mzcbor::QcborSpectrumPrecursor::getIsolationWindow

(

)

const

Definition at line 85 of file qcborspectrumprecursor.cpp.

{
  auto it = constFind(QCborValue("isolationWindow"));
  if(it != end())
    {
      IsolationWindow isolation_window;
      isolation_window.fromQCborMap(it->toMap());
      return isolation_window;
    }
  else
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR: no isolationWindow in QcborSpectrumPrecursor"));
    }
}

References pappso::cbor::mzcbor::IsolationWindow::fromQCborMap().

Referenced by FilterMs1WindowSelection::FilterMs1WindowSelection().

getSelectedIonList()

std::vector< SelectedIon > pappso::cbor::mzcbor::QcborSpectrumPrecursor::getSelectedIonList

(

)

const

Definition at line 159 of file qcborspectrumprecursor.cpp.

{
  std::vector<SelectedIon> selected_ion_list;
  auto itout = constFind(QCborValue("selectedIonList"));
  if(itout != end())
    {
      auto it = itout.value().toMap().constFind(QCborValue("selectedIon"));
      if(it != end())
        {
          for(auto it_cv = it->toArray().cbegin(); it_cv != it->toArray().cend(); it_cv++)
            {
              SelectedIon precursor;
              precursor.fromQCborMap(it_cv->toMap());
              selected_ion_list.push_back(precursor);
            }
          return selected_ion_list;
        }
      else
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR: no selectedIon array in QcborSpectrumPrecursor"));
        }
    }
  else
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR: no selectedIonList in QcborSpectrumPrecursor"));
    }
}

References pappso::cbor::mzcbor::SelectedIon::fromQCborMap().

Referenced by pappso::cbor::mzcbor::MzcborPrecursorFinder::findPotentialPrecursorIonData(), and pappso::cbor::mzcbor::MzcborPrecursorFinder::processQcborSpectrum().

getSpectrumRef()

QString pappso::cbor::mzcbor::QcborSpectrumPrecursor::getSpectrumRef

(

)

const

Definition at line 52 of file qcborspectrumprecursor.cpp.

{
  //"spectrumRef":"controllerType=0 controllerNumber=1 scan=2711",
  //
  auto it = constFind(QCborValue("spectrumRef"));
  if(it != end())
    {
      return it.value().toString();
    }
  else
    {
      throw pappso::ExceptionNotFound(
        QObject::tr("ERROR: no spectrumRef in QcborSpectrumPrecursor"));
    }
}

setSelectedIon()

void pappso::cbor::mzcbor::QcborSpectrumPrecursor::setSelectedIon	(	double	mz,
		double	intensity,
		int	charge )

Definition at line 102 of file qcborspectrumprecursor.cpp.

{
  auto it = find(QCborValue("selectedIonList"));
  if(it != end())
    {
      QCborMap new_selected_ion_list;
      new_selected_ion_list.insert(QString("count"), 1);
 
      QCborMap new_selected_ion;
      // <cvParam cvRef="MS" accession="MS:1000041" value="3" name="charge state"/>
      QCborArray cv_param_list;
      QCborMap cv_param;
      cv_param.insert(QString("cvRef"), QCborValue("MS"));
      cv_param.insert(QString("accession"), QCborValue("MS:1000041"));
      cv_param.insert(QString("value"), QCborValue(charge));
      cv_param.insert(QString("name"), QCborValue("charge state"));
      cv_param_list.push_back(cv_param);
      // <cvParam cvRef="MS" accession="MS:1000042" value="248032.25" name="peak intensity"
      // unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>
      //
      QCborMap cv_param_intensity;
      cv_param_intensity.insert(QString("cvRef"), QCborValue("MS"));
      cv_param_intensity.insert(QString("accession"), QCborValue("MS:1000042"));
      cv_param_intensity.insert(QString("value"), QCborValue(intensity));
      cv_param_intensity.insert(QString("name"), QCborValue("peak intensity"));
      cv_param_list.push_back(cv_param_intensity);
      // <cvParam
      // cvRef="MS" accession="MS:1000744" value="506.2513" name="selected ion m/z"
      // unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
      QCborMap cv_param_mz;
      cv_param_mz.insert(QString("cvRef"), QCborValue("MS"));
      cv_param_mz.insert(QString("accession"), QCborValue("MS:1000744"));
      cv_param_mz.insert(QString("value"), QCborValue(mz));
      cv_param_mz.insert(QString("name"), QCborValue("selected ion m/z"));
      cv_param_list.push_back(cv_param_mz);
 
      new_selected_ion.insert(QString("cvParam"), cv_param_list);
 
 
      QCborArray new_selected_ion_arr;
      new_selected_ion_arr.push_back(new_selected_ion);
 
 
      new_selected_ion_list.insert(QString("selectedIon"), new_selected_ion_arr);
      qDebug();
      // it.value() = new_selected_ion_list;
      insert(QCborValue("selectedIonList"), new_selected_ion_list);
      qDebug();
    }
 
  else
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR: no selectedIonList in QcborSpectrumPrecursor"));
    }
}

Referenced by pappso::cbor::mzcbor::MzcborPrecursorFinder::findPotentialPrecursorIonData().

setSpectrumRef()

void pappso::cbor::mzcbor::QcborSpectrumPrecursor::setSpectrumRef

(

const QString &

spectrum_ref

)

Definition at line 69 of file qcborspectrumprecursor.cpp.

{
  auto it = find(QCborValue("spectrumRef"));
  if(it != end())
    {
      insert(QCborValue("spectrumRef"), spectrum_ref);
    }
  else
    {
      throw pappso::ExceptionNotFound(
        QObject::tr("ERROR: no spectrumRef in QcborSpectrumPrecursor"));
    }
}

Referenced by pappso::cbor::mzcbor::MzcborPrecursorFinder::processQcborSpectrum().

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

• pappsomspp/core/processing/cbor/mzcbor/copyreplace/qcborspectrumprecursor.h
• pappsomspp/core/processing/cbor/mzcbor/copyreplace/qcborspectrumprecursor.cpp