pappso::cbor::psm::PsmSpecPeptidOmsScan Class Reference

#include <psmspecpeptidoms.h>

Inheritance diagram for pappso::cbor::psm::PsmSpecPeptidOmsScan:

Public Member Functions
	PsmSpecPeptidOmsScan (const PsmSpecPeptidOms &psm_specpeptidoms, pappso::PrecisionPtr fragment_tolerance)
virtual	~PsmSpecPeptidOmsScan ()
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
Protected Member Functions inherited from pappso::cbor::psm::CborScanMapBase
pappso::QualifiedMassSpectrumSPtr	getCurrentQualifiedMassSpectrumSPtr () const

Private Attributes
const PsmSpecPeptidOms *	mp_psmSpecPeptidOms
pappso::PrecisionPtr	m_fragmentTolerance
bool	m_checkMutations = false

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

Detailed Description

Definition at line 79 of file psmspecpeptidoms.h.

Constructor & Destructor Documentation

PsmSpecPeptidOmsScan()

pappso::cbor::psm::PsmSpecPeptidOmsScan::PsmSpecPeptidOmsScan	(	const PsmSpecPeptidOms &	psm_specpeptidoms,
		pappso::PrecisionPtr	fragment_tolerance )

Default constructor

Definition at line 97 of file psmspecpeptidoms.cpp.

  : CborScanMapBase(psm_specpeptidoms)
{
  m_fragmentTolerance = fragment_tolerance;
  mp_psmSpecPeptidOms = &psm_specpeptidoms;
}

References pappso::cbor::psm::CborScanMapBase::CborScanMapBase(), m_fragmentTolerance, and mp_psmSpecPeptidOms.

~PsmSpecPeptidOmsScan()

pappso::cbor::psm::PsmSpecPeptidOmsScan::~PsmSpecPeptidOmsScan ( )

virtual

Destructor

Definition at line 106 of file psmspecpeptidoms.cpp.

{
}

Member Function Documentation

process()

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

overrideprotectedvirtual

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

Definition at line 111 of file psmspecpeptidoms.cpp.

{
  // qDebug() << keys();
  if(!keys().contains("id"))
    {
      throw pappso::PappsoException(QObject::tr("missing scan id"));
    }
  if(keys().contains("psm_list"))
    {
      QualifiedMassSpectrumSPtr qualified_mass_spectrum = getCurrentQualifiedMassSpectrumSPtr();
 
 
      mp_psmSpecPeptidOms->filterMassSpectrum(
        *(qualified_mass_spectrum.get()->getMassSpectrumSPtr().get()));
 
      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_specglob;
          pappso::PeptideSp peptide_sp =
            pappso::PeptideProFormaParser::parseString(cbor_psm_map.value("proforma").toString());
 
 
          pappso::specpeptidoms::SpOMSSpectrumCsp experimental_spectrum =
            std::make_shared<pappso::specpeptidoms::SpOMSSpectrum>(
              *qualified_mass_spectrum.get(),
              m_fragmentTolerance,
              mp_psmSpecPeptidOms->getAaCode());
          /*
                    pappso::specglob::SpectralAlignment
             spectral_alignment(pappso::specglob::ScoreValues(), m_fragmentTolerance);
 
                    spectral_alignment.align(peptide_spectra, experimental_spectrum);
 
 
                    cbor_psm_eval_specglob.insert(QString("max_score"),
             spectral_alignment.getMaxScore());
 
 
                    if(spectral_alignment.getMaxScore() > 0)
                      {
                        pappso::specglob::PeptideModel peptide_model =
             spectral_alignment.buildPeptideModel();
 
                        // peptide_model.eliminateComplementaryDelta(m_fragmentTolerance);
                        // peptide_model.matchExperimentalPeaks(m_fragmentTolerance);
 
 
                        pappso::specglob::PostTreatment post_treatment(m_fragmentTolerance,
             peptide_model); if(m_checkMutations) post_treatment.findReplaceMutations();
                        peptide_model = post_treatment.getBetterPeptideModel();
 
                        cbor_psm_eval_specglob.insert(QString("count"),
                                                      (qint64)peptide_model.getCountSharedPeaks());
 
                        cbor_psm_eval_specglob.insert(QString("proforma"),
             peptide_model.toProForma()); cbor_psm_eval_specglob.insert(QString("bracket"),
             peptide_model.toString());
 
                        // peptide_model.checkForMutations()
                      }
 
 
                    QCborMap psm_eval = cbor_psm_map.value("eval").toMap();
                    psm_eval.remove(QString("specglob"));
                    psm_eval.insert(QString("specglob"), cbor_psm_eval_specglob);
                    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);
    }
}

References pappso::cbor::psm::CborScanMapBase::getCurrentQualifiedMassSpectrumSPtr(), m_fragmentTolerance, mp_psmSpecPeptidOms, and pappso::PeptideProFormaParser::parseString().

Member Data Documentation

m_checkMutations

bool pappso::cbor::psm::PsmSpecPeptidOmsScan::m_checkMutations = false

private

Definition at line 99 of file psmspecpeptidoms.h.

m_fragmentTolerance

pappso::PrecisionPtr pappso::cbor::psm::PsmSpecPeptidOmsScan::m_fragmentTolerance

private

Definition at line 98 of file psmspecpeptidoms.h.

Referenced by PsmSpecPeptidOmsScan(), and process().

mp_psmSpecPeptidOms

const PsmSpecPeptidOms* pappso::cbor::psm::PsmSpecPeptidOmsScan::mp_psmSpecPeptidOms

private

Definition at line 97 of file psmspecpeptidoms.h.

Referenced by PsmSpecPeptidOmsScan(), and process().

---

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

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