pappso::cbor::psm::CborScanMapBase Class Reference

#include <cborscanmapbase.h>

Inheritance diagram for pappso::cbor::psm::CborScanMapBase:

Public Member Functions
	CborScanMapBase (const PsmFileScanProcess &psm_file_scan_process)
virtual	~CborScanMapBase ()
virtual void	process ()
virtual void	filterAndSortPsmList ()
void	filterPsmListUniqueUniqueProforma ()
std::vector< double >::iterator	addPsmEvalVectorDouble (const QString &eval_name, const QString &eval_value_key, std::vector< double >::iterator begin, std::vector< double >::const_iterator end)
	add a new eval key and double values (from a vector) to each PSM
QCborMap	getCborScanId () const
QCborMap	getCborScanPrecursor () const
QCborArray	getCborPsmList () const
void	populateProteinMapUsingOldProteinMap (const PsmProteinMap &old_protein_map, PsmProteinMap &new_protein_map) const

Protected Member Functions
pappso::QualifiedMassSpectrumSPtr	getCurrentQualifiedMassSpectrumSPtr () const

Protected Attributes
const PsmFileScanProcess &	m_PsmFileScanProcess

Detailed Description

Todo

write docs

Definition at line 47 of file cborscanmapbase.h.

Constructor & Destructor Documentation

CborScanMapBase()

pappso::cbor::psm::CborScanMapBase::CborScanMapBase

(

const PsmFileScanProcess &

psm_file_scan_process

)

Default constructor

Definition at line 40 of file cborscanmapbase.cpp.

  : m_PsmFileScanProcess(psm_file_scan_process)
{
}

References m_PsmFileScanProcess.

Referenced by pappso::cbor::psm::PsmFeaturesScan::PsmFeaturesScan(), pappso::cbor::psm::PsmIonSeriesScan::PsmIonSeriesScan(), pappso::cbor::psm::PsmSpecGlobScan::PsmSpecGlobScan(), and pappso::cbor::psm::PsmSpecPeptidOmsScan::PsmSpecPeptidOmsScan().

~CborScanMapBase()

pappso::cbor::psm::CborScanMapBase::~CborScanMapBase ( )

virtual

Destructor

Definition at line 45 of file cborscanmapbase.cpp.

{
}

Member Function Documentation

addPsmEvalVectorDouble()

std::vector< double >::iterator pappso::cbor::psm::CborScanMapBase::addPsmEvalVectorDouble	(	const QString &	eval_name,
		const QString &	eval_value_key,
		std::vector< double >::iterator	begin,
		std::vector< double >::const_iterator	end )

add a new eval key and double values (from a vector) to each PSM

Definition at line 86 of file cborscanmapbase.cpp.

{
  std::vector<double>::iterator it = itbegin;
  if(keys().contains("psm_list"))
    {
 
 
      QCborArray new_psm_arr;
      for(QCborValue cbor_psm : value("psm_list").toArray())
        {
          QCborMap cbor_psm_map = cbor_psm.toMap();
 
          if(!cbor_psm_map.keys().contains("proforma"))
            {
              throw pappso::PappsoException(
                QObject::tr("missing proforma in psm %1").arg(cbor_psm_map.keys().size()));
            }
          QCborMap cbor_psm_eval_newvalues;
 
 
          if(it == itend)
            {
              throw pappso::PappsoException(
                QObject::tr("no more values to add in psm %1").arg(cbor_psm_map.keys().size()));
            }
          cbor_psm_eval_newvalues.insert(eval_value_key, *it);
          it++;
 
 
          QCborMap psm_eval = cbor_psm_map.value("eval").toMap();
          psm_eval.remove(eval_name);
          psm_eval.insert(eval_name, cbor_psm_eval_newvalues);
          cbor_psm_map.remove(QString("eval"));
          cbor_psm_map.insert(QString("eval"), psm_eval);
 
          new_psm_arr.push_back(cbor_psm_map);
        }
 
      // insert(QString("psm_list"), new_psm_arr);
      remove(QString("psm_list"));
      insert(QString("psm_list"), new_psm_arr);
    }
  return it;
}

Referenced by pappso::cbor::psm::PsmNewEval::newCborScanMap().

filterAndSortPsmList()

void pappso::cbor::psm::CborScanMapBase::filterAndSortPsmList ( )

virtual

Reimplemented in pappso::cbor::psm::PsmSpecPeptidOmsScan.

Definition at line 261 of file cborscanmapbase.cpp.

{
  // cbor_writer.writeCborMap(*this);
}

filterPsmListUniqueUniqueProforma()

void pappso::cbor::psm::CborScanMapBase::filterPsmListUniqueUniqueProforma

(

)

Definition at line 268 of file cborscanmapbase.cpp.

{
 
 
  struct uniquePsmResult
  {
    QString proforma;
    QCborMap psm;
  };
 
  QCborArray old_psm_arr = value("psm_list").toArray();
  QCborArray new_psm_arr;
  // for(QCborValue cbor_psm : old_psm_arr) {
 
 
  std::vector<uniquePsmResult> all_psm_list;
  for(auto it_psm : old_psm_arr)
    {
      QCborMap psm_map = it_psm.toMap();
      all_psm_list.push_back({psm_map.value("proforma").toString(), psm_map});
    }
  qDebug();
  std::sort(all_psm_list.begin(), all_psm_list.end(), [](uniquePsmResult &a, uniquePsmResult &b) {
    return a.proforma > b.proforma;
  });
 
  qDebug();
  std::vector<uniquePsmResult> unique_psm_list;
 
  for(auto it = all_psm_list.begin(); it != all_psm_list.end(); it++)
    {
      qDebug() << it->proforma;
      if(unique_psm_list.size() > 0)
        {
          if(unique_psm_list.back().proforma == it->proforma)
            {
              // merge ?
              PsmCborUtils::mergePsmProteinRefList(unique_psm_list.back().psm, it->psm);
            }
          else
            {
              unique_psm_list.push_back(*it);
            }
        }
      else
        {
          unique_psm_list.push_back(*it);
        }
 
      qDebug();
    }
 
 
  qDebug() << unique_psm_list.size();
  for(auto it = unique_psm_list.begin(); it != unique_psm_list.end(); it++)
    {
      new_psm_arr.append(it->psm);
      qDebug();
    }
 
  // qWarning() << new_psm_arr.size();
  remove(QString("psm_list"));
  insert(QString("psm_list"), new_psm_arr);
}

References pappso::a, pappso::b, and pappso::cbor::psm::PsmCborUtils::mergePsmProteinRefList().

Referenced by pappso::cbor::psm::PsmSpecGlobScan::process(), and pappso::cbor::psm::PsmSpecPeptidOmsScan::process().

getCborPsmList()

QCborArray pappso::cbor::psm::CborScanMapBase::getCborPsmList

(

)

const

Definition at line 75 of file cborscanmapbase.cpp.

{
  if(!keys().contains("psm_list"))
    {
      throw pappso::PappsoException(QObject::tr("missing psm_list in scan"));
    }
  return value("psm_list").toArray();
}

getCborScanId()

QCborMap pappso::cbor::psm::CborScanMapBase::getCborScanId

(

)

const

Definition at line 55 of file cborscanmapbase.cpp.

{
  if(!keys().contains("id"))
    {
      throw pappso::PappsoException(QObject::tr("missing id in scan"));
    }
  return value("id").toMap();
}

getCborScanPrecursor()

QCborMap pappso::cbor::psm::CborScanMapBase::getCborScanPrecursor

(

)

const

Definition at line 65 of file cborscanmapbase.cpp.

{
  if(!keys().contains("precursor"))
    {
      throw pappso::PappsoException(QObject::tr("missing precursor in scan"));
    }
  return value("precursor").toMap();
}

getCurrentQualifiedMassSpectrumSPtr()

pappso::QualifiedMassSpectrumSPtr pappso::cbor::psm::CborScanMapBase::getCurrentQualifiedMassSpectrumSPtr ( ) const

protected

Definition at line 136 of file cborscanmapbase.cpp.

{
  if(isEmpty())
    {
      throw pappso::PappsoException(QObject::tr("ERROR: cbor scan map is empty"));
    }
  if(!contains(QString("precursor")))
    {
      throw pappso::PappsoException(QObject::tr("ERROR: no precursor in scan"));
    }
  const QCborMap cbor_precursor(value("precursor").toMap());
  if(!contains(QString("ms2")))
    {
      throw pappso::PappsoException(QObject::tr("ERROR: ms2 is empty in scan"));
    }
  const QCborMap cbor_ms2(value("ms2").toMap());
 
  if(!contains(QString("id")))
    {
      throw pappso::PappsoException(QObject::tr("ERROR: id is empty in scan"));
    }
  const QCborMap cbor_id(value("id").toMap());
 
  if(!cbor_id.keys().contains("index"))
    {
      throw pappso::PappsoException("There is no scan index");
    }
 
  if(!cbor_ms2.keys().contains("spectrum"))
    {
      throw pappso::PappsoException("There is no spectrum in ms2");
    }
 
  const QCborMap cbor_spectrum(cbor_ms2.value("spectrum").toMap());
 
  if(!cbor_spectrum.keys().contains("mz"))
    {
      throw pappso::PappsoException("There is no cbor_spectrum mz values");
    }
  if(!cbor_spectrum.keys().contains("intensity"))
    {
      throw pappso::PappsoException("There is no cbor_spectrum intensity values");
    }
  pappso::MsRunId msrun_id(m_PsmFileScanProcess.m_currentPeaklistFile.name);
  msrun_id.setSampleName(m_PsmFileScanProcess.m_currentSampleName);
  pappso::MsRunIdCstSPtr msrun_id_sp = std::make_shared<const pappso::MsRunId>(msrun_id);
  pappso::MassSpectrumId ms_id(msrun_id_sp);
  ms_id.setSpectrumIndex(cbor_id.value("index").toInteger());
 
  // native_id
  if(cbor_id.keys().contains("native_id"))
    {
      ms_id.setNativeId(cbor_id.value("native_id").toString());
    }
 
  std::vector<DataPoint> data_point_vector;
  std::size_t i = 0;
  for(auto cbor_mz_value : cbor_spectrum.value("mz").toArray())
    {
      data_point_vector.push_back(
        {cbor_mz_value.toDouble(), cbor_spectrum.value("intensity").toArray().at(i).toDouble()});
      i++;
    }
 
 
  MassSpectrum mass_spectrum(data_point_vector);
  pappso::PrecursorIonData precursor_ion_data;
 
  pappso::QualifiedMassSpectrum qualified_mass_spectrum(ms_id);
  qualified_mass_spectrum.setMassSpectrumSPtr(mass_spectrum.makeMassSpectrumSPtr());
  qualified_mass_spectrum.setMsLevel(2);
 
  if(cbor_precursor.keys().contains("z"))
    {
      precursor_ion_data.charge = cbor_precursor.value("z").toInteger();
    }
  if(cbor_precursor.keys().contains("mz"))
    {
      precursor_ion_data.mz = cbor_precursor.value("mz").toDouble();
    }
  if(cbor_precursor.keys().contains("intensity"))
    {
      precursor_ion_data.intensity = cbor_precursor.value("intensity").toDouble();
    }
  qualified_mass_spectrum.appendPrecursorIonData(precursor_ion_data);
  if(cbor_ms2.keys().contains("rt"))
    {
      qualified_mass_spectrum.setRtInSeconds(cbor_ms2.value("rt").toDouble());
    }
 
 
  return qualified_mass_spectrum.makeQualifiedMassSpectrumSPtr();
}

References pappso::QualifiedMassSpectrum::appendPrecursorIonData(), pappso::PrecursorIonData::charge, pappso::PrecursorIonData::intensity, m_PsmFileScanProcess, pappso::MassSpectrum::makeMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumSPtr(), pappso::PrecursorIonData::mz, pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MsRunId::setSampleName(), and pappso::MassSpectrumId::setSpectrumIndex().

Referenced by pappso::cbor::psm::PsmFeaturesScan::process(), pappso::cbor::psm::PsmIonSeriesScan::process(), pappso::cbor::psm::PsmSpecGlobScan::process(), and pappso::cbor::psm::PsmSpecPeptidOmsScan::process().

populateProteinMapUsingOldProteinMap()

void pappso::cbor::psm::CborScanMapBase::populateProteinMapUsingOldProteinMap	(	const PsmProteinMap &	old_protein_map,
		PsmProteinMap &	new_protein_map ) const

Definition at line 230 of file cborscanmapbase.cpp.

{
  if(isEmpty())
    {
      throw pappso::PappsoException(QObject::tr("ERROR: cbor scan map is empty"));
    }
  if(!contains(QString("psm_list")))
    {
      throw pappso::PappsoException(QObject::tr("ERROR: no psm_list in scan"));
    }
 
  for(auto it_psm : value("psm_list").toArray())
    {
      QCborMap psm = it_psm.toMap();
      if(!psm.contains(QString("protein_list")))
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR: no protein_list in psm, psm_list in scan"));
        }
 
      for(auto it_protein : psm.value("protein_list").toArray())
        {
          new_protein_map.insert(
            old_protein_map.getByAccession(it_protein.toMap().value("accession").toString()));
        }
    }
}

References pappso::cbor::psm::PsmProteinMap::getByAccession(), and pappso::cbor::psm::PsmProteinMap::insert().

process()

void pappso::cbor::psm::CborScanMapBase::process ( )

virtual

Reimplemented in pappso::cbor::psm::PsmFeaturesScan, pappso::cbor::psm::PsmIonSeriesScan, pappso::cbor::psm::PsmSpecGlobScan, and pappso::cbor::psm::PsmSpecPeptidOmsScan.

Definition at line 50 of file cborscanmapbase.cpp.

{
}

Member Data Documentation

m_PsmFileScanProcess

const PsmFileScanProcess& pappso::cbor::psm::CborScanMapBase::m_PsmFileScanProcess

protected

Definition at line 85 of file cborscanmapbase.h.

Referenced by CborScanMapBase(), and getCurrentQualifiedMassSpectrumSPtr().

---

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

• pappsomspp/core/processing/cbor/psm/cborscanmapbase.h
• pappsomspp/core/processing/cbor/psm/cborscanmapbase.cpp