pappso::cbor::psm::PsmSpecGlobScan Class Reference

#include <psmspecglobscan.h>

Inheritance diagram for pappso::cbor::psm::PsmSpecGlobScan:

Public Member Functions
	PsmSpecGlobScan (const PsmSpecGlob &psm_specgloc, pappso::PrecisionPtr fragment_tolerance)
virtual	~PsmSpecGlobScan ()
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
Protected Member Functions inherited from pappso::cbor::psm::CborScanMapBase
pappso::QualifiedMassSpectrumSPtr	getCurrentQualifiedMassSpectrumSPtr () const

Private Attributes
const PsmSpecGlob *	mp_psmSpecGlob
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

Todo

write docs

Definition at line 37 of file psmspecglobscan.h.

Constructor & Destructor Documentation

PsmSpecGlobScan()

pappso::cbor::psm::PsmSpecGlobScan::PsmSpecGlobScan	(	const PsmSpecGlob &	psm_specgloc,
		pappso::PrecisionPtr	fragment_tolerance )

Default constructor

Definition at line 35 of file psmspecglobscan.cpp.

  : CborScanMapBase(psm_specgloc)
{
  m_fragmentTolerance = fragment_tolerance;
  mp_psmSpecGlob      = &psm_specgloc;
}

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

~PsmSpecGlobScan()

pappso::cbor::psm::PsmSpecGlobScan::~PsmSpecGlobScan ( )

virtual

Destructor

Definition at line 43 of file psmspecglobscan.cpp.

{
}

Member Function Documentation

process()

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

overrideprotectedvirtual

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

Definition at line 48 of file psmspecglobscan.cpp.

{
  if(!keys().contains("id"))
    {
      throw pappso::PappsoException(QObject::tr("missing scan id"));
    }
  if(keys().contains("psm_list"))
    {
      QualifiedMassSpectrumSPtr qualified_mass_spectrum = getCurrentQualifiedMassSpectrumSPtr();
      pappso::specglob::ExperimentalSpectrumCsp experimental_spectrum =
        std::make_shared<pappso::specglob::ExperimentalSpectrum>(*qualified_mass_spectrum.get(),
                                                                 m_fragmentTolerance);
 
 
      mp_psmSpecGlob->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 spectrum %2")
                  .arg(cbor_psm_map.keys().size())
                  .arg(qualified_mass_spectrum.get()->getMassSpectrumId().getNativeId()));
            }
          QString proforma = cbor_psm_map.value("proforma").toString();
          if(proforma.isEmpty())
            {
 
              throw pappso::PappsoException(
                QObject::tr("proforma is empty in psm %1 spectrum %2")
                  .arg(cbor_psm_map.keys().size())
                  .arg(qualified_mass_spectrum.get()->getMassSpectrumId().getNativeId()));
            }
          QCborMap cbor_psm_eval_specglob;
          qDebug();
          pappso::PeptideSp peptide_sp = pappso::PeptideProFormaParser::parseString(proforma);
 
          qDebug() << proforma << " " << peptide_sp.get()->toProForma();
          pappso::specglob::PeptideSpectraCsp peptide_spectra =
            std::make_shared<pappso::specglob::PeptideSpectrum>(peptide_sp);
 
          qDebug();
 
          qDebug();
          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());
 
          bool keep = false;
 
          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()
 
              if(mp_psmSpecGlob->m_isProteinMatcherResult)
                {
                  keep = true;
                }
            }
 
          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);
 
          if(mp_psmSpecGlob->m_isProteinMatcherResult)
            {
              if(keep)
                {
                  QCborMap new_psm;
                  new_psm.insert(QString("proforma"),
                                 cbor_psm_eval_specglob.value("proforma").toString());
                  new_psm.insert(QString("protein_list"), cbor_psm_map.value("protein_list"));
                  new_psm.insert(QString("eval"), cbor_psm_map.value("eval"));
                  new_psm_arr.push_back(new_psm);
                }
            }
          else
            {
              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);
 
 
      filterPsmListUniqueUniqueProforma();
    }
}

References pappso::specglob::SpectralAlignment::align(), pappso::specglob::SpectralAlignment::buildPeptideModel(), pappso::cbor::psm::CborScanMapBase::filterPsmListUniqueUniqueProforma(), pappso::specglob::PostTreatment::findReplaceMutations(), pappso::specglob::PostTreatment::getBetterPeptideModel(), pappso::specglob::PeptideModel::getCountSharedPeaks(), pappso::cbor::psm::CborScanMapBase::getCurrentQualifiedMassSpectrumSPtr(), pappso::specglob::SpectralAlignment::getMaxScore(), m_checkMutations, m_fragmentTolerance, mp_psmSpecGlob, pappso::PeptideProFormaParser::parseString(), pappso::specglob::PeptideModel::toProForma(), and pappso::specglob::PeptideModel::toString().

Member Data Documentation

m_checkMutations

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

private

Definition at line 57 of file psmspecglobscan.h.

Referenced by process().

m_fragmentTolerance

pappso::PrecisionPtr pappso::cbor::psm::PsmSpecGlobScan::m_fragmentTolerance

private

Definition at line 56 of file psmspecglobscan.h.

Referenced by PsmSpecGlobScan(), and process().

mp_psmSpecGlob

const PsmSpecGlob* pappso::cbor::psm::PsmSpecGlobScan::mp_psmSpecGlob

private

Definition at line 55 of file psmspecglobscan.h.

Referenced by PsmSpecGlobScan(), and process().

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

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