pappso::cbor::psm::PsmFeaturesScan Class Reference

#include <psmfeaturesscan.h>

Inheritance diagram for pappso::cbor::psm::PsmFeaturesScan:

Public Member Functions
	PsmFeaturesScan (const PsmFileScanProcess &psm_file_scan_process, pappso::XtandemSpectrumProcess &tandem_spectrum_process, std::list< pappso::Enums::PeptideIon > &ion_list, pappso::PsmFeatures &psm_features, pappso::PrecisionPtr fragment_tolerance)
virtual	~PsmFeaturesScan ()
Public Member Functions inherited from pappso::cbor::psm::CborScanMapBase
	CborScanMapBase (const PsmFileScanProcess &psm_file_scan_process)
virtual	~CborScanMapBase ()
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
void	process () override
double	checkInf (double input) const
Protected Member Functions inherited from pappso::cbor::psm::CborScanMapBase
pappso::QualifiedMassSpectrumSPtr	getCurrentQualifiedMassSpectrumSPtr () const

Private Attributes
pappso::XtandemSpectrumProcess &	m_tandemSpectrumProcess
std::list< pappso::Enums::PeptideIon > &	m_ionList
pappso::PsmFeatures	m_psmFeatures
pappso::PrecisionPtr	m_fragmentTolerance

Additional Inherited Members
Protected Attributes inherited from pappso::cbor::psm::CborScanMapBase
const PsmFileScanProcess &	m_PsmFileScanProcess

Detailed Description

Todo:

write docs

Definition at line 44 of file psmfeaturesscan.h.

Constructor & Destructor Documentation

PsmFeaturesScan()

pappso::cbor::psm::PsmFeaturesScan::PsmFeaturesScan	(	const PsmFileScanProcess &	psm_file_scan_process,
		pappso::XtandemSpectrumProcess &	tandem_spectrum_process,
		std::list< pappso::Enums::PeptideIon > &	ion_list,
		pappso::PsmFeatures &	psm_features,
		pappso::PrecisionPtr	fragment_tolerance
	)

Default constructor

Definition at line 42 of file psmfeaturesscan.cpp.

  : CborScanMapBase(psm_file_scan_process),
    m_tandemSpectrumProcess(tandem_spectrum_process),
    m_ionList(ion_list),
    m_psmFeatures(psm_features)
{
  m_fragmentTolerance = fragment_tolerance;
}

References m_fragmentTolerance.

~PsmFeaturesScan()

pappso::cbor::psm::PsmFeaturesScan::~PsmFeaturesScan ( )

virtual

Destructor

Definition at line 55 of file psmfeaturesscan.cpp.

{
}

Member Function Documentation

checkInf()

double pappso::cbor::psm::PsmFeaturesScan::checkInf ( double  input ) const

protected

Definition at line 60 of file psmfeaturesscan.cpp.

{
  if(input < 0)
    return 0;
  return input;
}

Referenced by process().

process()

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

overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::CborScanMapBase.

Definition at line 68 of file psmfeaturesscan.cpp.

{
 
  if(keys().contains("psm_list"))
    {
      QualifiedMassSpectrumSPtr qualified_mass_spectrum = getCurrentQualifiedMassSpectrumSPtr();
 
      pappso::MassSpectrum spectrum =
        m_tandemSpectrumProcess.process(*qualified_mass_spectrum.get()->getMassSpectrumSPtr().get(),
                                        qualified_mass_spectrum.get()->getPrecursorMz(),
                                        qualified_mass_spectrum.get()->getPrecursorCharge());
 
      // qWarning() << qualified_mass_spectrum.get()->getMassSpectrumId().getSpectrumIndex();
      QCborArray new_psm_arr;
      for(QCborValue cbor_psm : value("psm_list").toArray())
        {
          QCborMap cbor_psm_map = cbor_psm.toMap();
          QCborMap cbor_psm_features;
          pappso::PeptideSp peptide_sp =
            pappso::PeptideProFormaParser::parseString(cbor_psm_map.value("proforma").toString());
 
          if(peptide_sp.get()->size() < 2)
            {
              throw pappso::PappsoException(QObject::tr("peptide in psm too small %1")
                                              .arg(cbor_psm_map.value("proforma").toString()));
            }
          // qWarning() << cbor_psm_map.value("proforma").toString() << "end " <<
          // qualified_mass_spectrum.get()->getMassSpectrumId().getSpectrumIndex();
 
          std::size_t peptide_size = peptide_sp.get()->size();
          cbor_psm_features.insert(QString("peptide_size"), (unsigned int)peptide_size);
 
          pappso::XtandemHyperscore hyperscore(spectrum,
                                               peptide_sp,
                                               qualified_mass_spectrum.get()->getPrecursorCharge(),
                                               m_fragmentTolerance,
                                               m_ionList,
                                               true);
          cbor_psm_features.insert(QString("hyperscore"), QCborValue(hyperscore.getHyperscore()));
          // qWarning() << cbor_psm_map.value("proforma").toString() << "end2 " <<
          // qualified_mass_spectrum.get()->getMassSpectrumId().getSpectrumIndex();
 
          m_psmFeatures.setPeptideSpectrumCharge(
            peptide_sp,
            qualified_mass_spectrum.get()->getMassSpectrumSPtr().get(),
            qualified_mass_spectrum.get()->getPrecursorCharge(),
            2);
          // TIC
          cbor_psm_features.insert(QString("total_intensity"),
                                   std::log(m_psmFeatures.getTotalIntensity()));
          // MaxIntALL
          cbor_psm_features.insert(QString("max_intensity"),
                                   checkInf(std::log(qualified_mass_spectrum.get()
                                                       ->getMassSpectrumSPtr()
                                                       .get()
                                                       ->maxIntensityDataPoint()
                                                       .y)));
 
          // qWarning() << cbor_psm_map.value("proforma").toString() << "end3 " <<
          // qualified_mass_spectrum.get()->getMassSpectrumId().getSpectrumIndex();
          //  MaxYionInt
          cbor_psm_features.insert(
            QString("MaxYionInt"),
            checkInf(std::log(m_psmFeatures.getMaxIntensityPeakIonMatch(Enums::PeptideIon::y))));
 
          // MaxBionInt
          cbor_psm_features.insert(
            QString("MaxBionInt"),
            checkInf(std::log(m_psmFeatures.getMaxIntensityPeakIonMatch(Enums::PeptideIon::b))));
 
          // SumYmatchInt
          cbor_psm_features.insert(
            QString("SumYmatchInt"),
            checkInf(std::log(m_psmFeatures.getIntensityOfMatchedIon(Enums::PeptideIon::y))));
 
          // SumBmatchInt
          cbor_psm_features.insert(
            QString("SumBmatchInt"),
            checkInf(std::log(m_psmFeatures.getIntensityOfMatchedIon(Enums::PeptideIon::b))));
 
          // FracYmatchInt
          cbor_psm_features.insert(
            QString("FracYmatchInt"),
            checkInf(m_psmFeatures.getIntensityOfMatchedIon(Enums::PeptideIon::y) /
                     m_psmFeatures.getTotalIntensity()));
          // FracBmatchInt
          cbor_psm_features.insert(
            QString("FracBmatchInt"),
            checkInf(m_psmFeatures.getIntensityOfMatchedIon(Enums::PeptideIon::b) /
                     m_psmFeatures.getTotalIntensity()));
 
          // SeqCoverYion
          cbor_psm_features.insert(
            QString("SeqCoverYion"),
            (double)m_psmFeatures.getAaSequenceCoverage(Enums::PeptideIon::y) /
              (double)peptide_size);
          // SeqCoverBion
          cbor_psm_features.insert(
            QString("SeqCoverBion"),
            (double)m_psmFeatures.getAaSequenceCoverage(Enums::PeptideIon::b) /
              (double)peptide_size);
 
 
          // ConsecutiveYion
          cbor_psm_features.insert(
            QString("ConsecutiveYion"),
            (qint64)m_psmFeatures.getMaxConsecutiveIon(Enums::PeptideIon::y));
          // ConsecutiveBion
          cbor_psm_features.insert(
            QString("ConsecutiveBion"),
            (qint64)m_psmFeatures.getMaxConsecutiveIon(Enums::PeptideIon::b));
 
          // MassErrMean
          cbor_psm_features.insert(QString("MassErrMean"), m_psmFeatures.getMatchedMzDiffMean());
 
          // MassErrSD
          cbor_psm_features.insert(QString("MassErrSD"), m_psmFeatures.getMatchedMzDiffSd());
 
          // NumofAnnoPeaks
          cbor_psm_features.insert(QString("NumofAnnoPeaks"),
                                   (unsigned int)m_psmFeatures.getNumberOfMatchedIons());
 
          // qWarning() << cbor_psm_map.value("proforma").toString() << "end2 " <<
          // qualified_mass_spectrum.get()->getMassSpectrumId().getSpectrumIndex();
          //  NumofComplementPeaks
          std::size_t num_of_pairs = m_psmFeatures.countMatchedIonComplementPairs();
          cbor_psm_features.insert(QString("NumofComplementPeaks"), (unsigned int)num_of_pairs);
          if(num_of_pairs > 0)
            {
              // SumComplementPeaksInt
              cbor_psm_features.insert(
                QString("SumComplementPeaksInt"),
                std::log(m_psmFeatures.getTotalIntensityOfMatchedIonComplementPairs()));
 
              // FracComplementPeaksInt
              cbor_psm_features.insert(
                QString("FracComplementPeaksInt"),
                m_psmFeatures.getTotalIntensityOfMatchedIonComplementPairs() /
                  m_psmFeatures.getTotalIntensity());
              // SeqCoverComplementPeaks
              cbor_psm_features.insert(
                QString("SeqCoverComplementPeaks"),
                (double)m_psmFeatures.getComplementPairsAaSequenceCoverage() /
                  (double)peptide_size);
            }
          pappso::LinearRegression lr = m_psmFeatures.getIonIsotopeLinearRegression();
          cbor_psm_features.insert(QString("lrSize"), (unsigned int)lr.getSize());
 
 
          double coeff_of_determination = lr.getCoefficientOfDetermination();
          if(std::isnan(coeff_of_determination))
            {
            }
          else
            {
              cbor_psm_features.insert(QString("lrCoeffDet"), coeff_of_determination);
            }
 
 
          QCborMap psm_eval = cbor_psm_map.value("eval").toMap();
          psm_eval.remove(QString("features"));
          psm_eval.insert(QString("features"), cbor_psm_features);
          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);
      // qWarning() << "end " <<
      // qualified_mass_spectrum.get()->getMassSpectrumId().getSpectrumIndex();
    }
}

References pappso::Enums::b, checkInf(), pappso::PsmFeatures::countMatchedIonComplementPairs(), pappso::PsmFeatures::getAaSequenceCoverage(), pappso::LinearRegression::getCoefficientOfDetermination(), pappso::PsmFeatures::getComplementPairsAaSequenceCoverage(), pappso::cbor::psm::CborScanMapBase::getCurrentQualifiedMassSpectrumSPtr(), pappso::XtandemHyperscore::getHyperscore(), pappso::PsmFeatures::getIntensityOfMatchedIon(), pappso::PsmFeatures::getIonIsotopeLinearRegression(), pappso::PsmFeatures::getMatchedMzDiffMean(), pappso::PsmFeatures::getMatchedMzDiffSd(), pappso::PsmFeatures::getMaxConsecutiveIon(), pappso::PsmFeatures::getMaxIntensityPeakIonMatch(), pappso::PsmFeatures::getNumberOfMatchedIons(), pappso::LinearRegression::getSize(), pappso::PsmFeatures::getTotalIntensity(), pappso::PsmFeatures::getTotalIntensityOfMatchedIonComplementPairs(), m_fragmentTolerance, m_ionList, m_psmFeatures, m_tandemSpectrumProcess, pappso::PeptideProFormaParser::parseString(), pappso::XtandemSpectrumProcess::process(), pappso::PsmFeatures::setPeptideSpectrumCharge(), pappso::Trace::toMap(), and pappso::Enums::y.

Member Data Documentation

m_fragmentTolerance

pappso::PrecisionPtr pappso::cbor::psm::PsmFeaturesScan::m_fragmentTolerance

private

Definition at line 69 of file psmfeaturesscan.h.

Referenced by PsmFeaturesScan(), and process().

m_ionList

std::list<pappso::Enums::PeptideIon>& pappso::cbor::psm::PsmFeaturesScan::m_ionList

private

Definition at line 67 of file psmfeaturesscan.h.

Referenced by process().

m_psmFeatures

pappso::PsmFeatures pappso::cbor::psm::PsmFeaturesScan::m_psmFeatures

private

Definition at line 68 of file psmfeaturesscan.h.

Referenced by process().

m_tandemSpectrumProcess

pappso::XtandemSpectrumProcess& pappso::cbor::psm::PsmFeaturesScan::m_tandemSpectrumProcess

private

Definition at line 66 of file psmfeaturesscan.h.

Referenced by process().

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

• pappsomspp/core/processing/cbor/psm/evalscan/psmfeaturesscan.h
• pappsomspp/core/processing/cbor/psm/evalscan/psmfeaturesscan.cpp