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::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	process ()
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 More...
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::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 38 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::PeptideIon > &	ion_list,
		pappso::PsmFeatures &	psm_features,
		pappso::PrecisionPtr	fragment_tolerance
	)

Default constructor

Definition at line 35 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 49 of file psmfeaturesscan.cpp.

{
}

Member Function Documentation

checkInf()

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

protected

Definition at line 54 of file psmfeaturesscan.cpp.

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

process()

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

overrideprotectedvirtual

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

Definition at line 62 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(pappso::PeptideIon::y))));
 
          // MaxBionInt
          cbor_psm_features.insert(
            QString("MaxBionInt"),
            checkInf(std::log(m_psmFeatures.getMaxIntensityPeakIonMatch(pappso::PeptideIon::b))));
 
          // SumYmatchInt
          cbor_psm_features.insert(
            QString("SumYmatchInt"),
            checkInf(std::log(m_psmFeatures.getIntensityOfMatchedIon(pappso::PeptideIon::y))));
 
          // SumBmatchInt
          cbor_psm_features.insert(
            QString("SumBmatchInt"),
            checkInf(std::log(m_psmFeatures.getIntensityOfMatchedIon(pappso::PeptideIon::b))));
 
          // FracYmatchInt
          cbor_psm_features.insert(
            QString("FracYmatchInt"),
            checkInf(m_psmFeatures.getIntensityOfMatchedIon(pappso::PeptideIon::y) /
                     m_psmFeatures.getTotalIntensity()));
          // FracBmatchInt
          cbor_psm_features.insert(
            QString("FracBmatchInt"),
            checkInf(m_psmFeatures.getIntensityOfMatchedIon(pappso::PeptideIon::b) /
                     m_psmFeatures.getTotalIntensity()));
 
          // SeqCoverYion
          cbor_psm_features.insert(
            QString("SeqCoverYion"),
            (double)m_psmFeatures.getAaSequenceCoverage(pappso::PeptideIon::y) /
              (double)peptide_size);
          // SeqCoverBion
          cbor_psm_features.insert(
            QString("SeqCoverBion"),
            (double)m_psmFeatures.getAaSequenceCoverage(pappso::PeptideIon::b) /
              (double)peptide_size);
 
 
          // ConsecutiveYion
          cbor_psm_features.insert(
            QString("ConsecutiveYion"),
            (qint64)m_psmFeatures.getMaxConsecutiveIon(pappso::PeptideIon::y));
          // ConsecutiveBion
          cbor_psm_features.insert(
            QString("ConsecutiveBion"),
            (qint64)m_psmFeatures.getMaxConsecutiveIon(pappso::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);
    }
}

References pappso::b, pappso::LinearRegression::getCoefficientOfDetermination(), pappso::XtandemHyperscore::getHyperscore(), pappso::LinearRegression::getSize(), pappso::PeptideProFormaParser::parseString(), pappso::Trace::toMap(), and pappso::y.

Member Data Documentation

m_fragmentTolerance

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

private

Definition at line 63 of file psmfeaturesscan.h.

Referenced by PsmFeaturesScan().

m_ionList

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

private

Definition at line 61 of file psmfeaturesscan.h.

m_psmFeatures

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

private

Definition at line 62 of file psmfeaturesscan.h.

m_tandemSpectrumProcess

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

private

Definition at line 60 of file psmfeaturesscan.h.

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

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