#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 ()

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

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.

56{

57}

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());
 
      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());
 
 
          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()));
 
 
          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)));
 
          // 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());
 
          // 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);
    }
}

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().

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

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PsmFeaturesScan()

◆ ~PsmFeaturesScan()

Member Function Documentation

◆ checkInf()

◆ process()

Member Data Documentation

◆ m_fragmentTolerance

◆ m_ionList

◆ m_psmFeatures

◆ m_tandemSpectrumProcess