pappso::cbor::psm::PsmSpecPeptidOms Class Reference

#include <psmspecpeptidoms.h>

Inheritance diagram for pappso::cbor::psm::PsmSpecPeptidOms:

Public Member Functions
	PsmSpecPeptidOms (std::size_t buffer_scan_size, CborStreamWriter *cbor_output_p, const QJsonObject &parameters)
virtual	~PsmSpecPeptidOms ()
void	filterMassSpectrum (pappso::MassSpectrum &mass_spectrum) const
const pappso::AaCode &	getAaCode () const
Public Member Functions inherited from pappso::cbor::psm::PsmFileScanProcessAndCopy
	PsmFileScanProcessAndCopy (std::size_t buffer_scan_size, CborStreamWriter *cbor_output_p, const QString &operation)
virtual	~PsmFileScanProcessAndCopy ()
void	close () override
	convenient function to clean pointer before leaving
Public Member Functions inherited from pappso::cbor::psm::PsmFileScanProcess
	PsmFileScanProcess (std::size_t buffer_scan_size)
virtual	~PsmFileScanProcess ()
Public Member Functions inherited from pappso::cbor::psm::PsmFileReaderBase
	PsmFileReaderBase ()
virtual	~PsmFileReaderBase () override
void	readCbor (QFile *cborp, pappso::UiMonitorInterface &monitor)
void	readCbor (QIODevice *cborp, pappso::UiMonitorInterface &monitor)
Public Member Functions inherited from pappso::cbor::CborStreamReaderInterface
	CborStreamReaderInterface ()
virtual	~CborStreamReaderInterface ()

Protected Member Functions
CborScanMapBase *	newCborScanMap () override
void	parameterMapReady (pappso::UiMonitorInterface &monitor) override
virtual void	processBufferScanDone (pappso::UiMonitorInterface &monitor) override
virtual void	proteinMapReady (pappso::UiMonitorInterface &monitor) override
Protected Member Functions inherited from pappso::cbor::psm::PsmFileScanProcessAndCopy
void	delayProteinMapInMemory ()
void	informationsReady (pappso::UiMonitorInterface &monitor) override
void	logReady (pappso::UiMonitorInterface &monitor) override
void	fastaFilesReady (pappso::UiMonitorInterface &monitor) override
void	sampleStarted (pappso::UiMonitorInterface &monitor) override
void	sampleFinished (pappso::UiMonitorInterface &monitor) override
void	sampleListStarted (pappso::UiMonitorInterface &monitor) override
void	sampleListFinished (pappso::UiMonitorInterface &monitor) override
Protected Member Functions inherited from pappso::cbor::psm::PsmFileScanProcess
void	readScan (pappso::UiMonitorInterface &monitor) override
void	scanFinished (pappso::UiMonitorInterface &monitor) override
virtual void	processBufferScan (pappso::UiMonitorInterface &monitor)
void	clearScanBuffer ()
Protected Member Functions inherited from pappso::cbor::psm::PsmFileReaderBase
void	readRoot (pappso::UiMonitorInterface &monitor)
virtual void	readInformations (pappso::UiMonitorInterface &monitor)
virtual void	readLog (pappso::UiMonitorInterface &monitor)
virtual void	readParameterMap (pappso::UiMonitorInterface &monitor)
virtual void	readProteinMap (pappso::UiMonitorInterface &monitor)
virtual void	readSample (pappso::UiMonitorInterface &monitor)
virtual void	readPsm (pappso::UiMonitorInterface &monitor)
virtual void	psmReady (pappso::UiMonitorInterface &monitor)
virtual void	scanStarted (pappso::UiMonitorInterface &monitor)
PsmFile	readPsmFile (bool &is_ok)
void	writePsmFile (CborStreamWriter &writer, const PsmFile &psm_file)
void	writePsmFileList (CborStreamWriter &writer, const std::vector< PsmFile > &file_list)
PsmProteinRef	readPsmProteinRef (bool &is_ok)
pappso::PeptideSp	getCurrentPsmPeptideSp () const
pappso::QualifiedMassSpectrumSPtr	getCurrentQualifiedMassSpectrumSPtr () const
	get the qualified Spectrum for the current PSM
bool	currentProteinRefListContainsDecoy () const
	tells if the current PSM has a decoy accession
bool	currentProteinRefListContainsTarget () const
	tells if the current PSM has a target accession
double	getPrecursorMass (double mz_prec, uint charge) const
	convenient function do compute precusor ion mass
Protected Member Functions inherited from pappso::cbor::CborStreamReaderInterface
bool	getExpectedString ()
void	initCborReader (QFile *pcborfile)
void	initCborReader (QIODevice *pcborfile)

Protected Attributes
pappso::AaCode	m_aaCode
QJsonObject	m_specpeptidomsParameters
pappso::PrecisionPtr	m_fragmentTolerance
double	m_minimumMz
std::size_t	m_nMostIntense
bool	m_deisotope = true
pappso::specpeptidoms::ScoreValues	m_scoreValues
std::size_t	m_countScanProcessed = 0
pappso::cbor::psm::PsmProteinMap	m_newProteinMap
QString	m_decoyPrefix
std::size_t	m_maxInterpretationsPerSpectrum = 1
Protected Attributes inherited from pappso::cbor::psm::PsmFileScanProcessAndCopy
CborStreamWriter *	mp_cborOutput
CborStreamWriter *	mp_copyCborOutput = nullptr
QString	m_operation
pappso::cbor::psm::PsmProteinMap	m_psmNewProteinMap
QBuffer *	mpa_bufferAfterProteinMap = nullptr
pappso::cbor::CborStreamWriter *	mpa_bufferWriterAfterProteinMap = nullptr
Protected Attributes inherited from pappso::cbor::psm::PsmFileScanProcess
std::size_t	m_bufferScanSize = 1000
std::vector< CborScanMapBase * >	m_cborScanList
Protected Attributes inherited from pappso::cbor::psm::PsmFileReaderBase
QStringList	m_targetFastaFiles
QStringList	m_decoyFastaFiles
PsmProteinMap	m_proteinMap
QString	m_currentSampleName
PsmFile	m_currentPeaklistFile
std::vector< PsmFile >	m_currentIdentificationFileList
QCborMap	m_cborInformations
QCborArray	m_cborLog
QCborMap	m_cborParameterMap
QCborMap	m_cborScanId
QCborMap	m_cborScanPrecursor
QCborMap	m_cborScanMs2
QCborMap	m_cborScanProps
QCborMap	m_cborScanPsmEval
QCborMap	m_cborScanPsmProps
QString	m_currentPsmProforma
std::vector< PsmProteinRef >	m_currentPsmProteinRefList
Protected Attributes inherited from pappso::cbor::CborStreamReaderInterface
CborStreamReader *	mpa_cborReader = nullptr
QString	m_expectedString
QByteArray	m_data

Private Attributes
friend	PsmSpecPeptidOmsScan

Detailed Description

Todo

write docs

Definition at line 48 of file psmspecpeptidoms.h.

Constructor & Destructor Documentation

PsmSpecPeptidOms()

pappso::cbor::psm::PsmSpecPeptidOms::PsmSpecPeptidOms	(	std::size_t	buffer_scan_size,
		CborStreamWriter *	cbor_output_p,
		const QJsonObject &	parameters )

Default constructor

Definition at line 40 of file psmspecpeptidoms.cpp.

  : PsmFileScanProcessAndCopy(buffer_scan_size, cbor_output_p, "SpecPeptidOms")
{
  m_specpeptidomsParameters = parameters;
 
  if(parameters.value("fragment_tolerance_unit").toString() == "dalton")
    {
      m_fragmentTolerance = pappso::PrecisionFactory::getDaltonInstance(
        parameters.value("fragment_tolerance").toDouble());
    }
  else if(parameters.value("fragment_tolerance_unit").toString() == "ppm")
    {
      m_fragmentTolerance =
        pappso::PrecisionFactory::getPpmInstance(parameters.value("fragment_tolerance").toDouble());
    }
 
  QJsonObject spectrum_param = parameters.value("spectrum").toObject();
 
  m_minimumMz    = spectrum_param.value("minimum_mz").toDouble();
  m_nMostIntense = spectrum_param.value("n_most_intense").toInt();
  m_deisotope    = spectrum_param.value("deisotope").toBool();
 
  m_aaCode.addAaModification('C', AaModification::getInstance("MOD:00397"));
 
 
  m_maxInterpretationsPerSpectrum = parameters.value("max_interpretations_per_spectrum").toInt();
 
  delayProteinMapInMemory();
}

References pappso::cbor::psm::PsmFileScanProcessAndCopy::PsmFileScanProcessAndCopy(), pappso::cbor::psm::PsmFileScanProcessAndCopy::delayProteinMapInMemory(), pappso::AaModification::getInstance(), m_aaCode, m_deisotope, m_maxInterpretationsPerSpectrum, m_minimumMz, m_nMostIntense, and m_specpeptidomsParameters.

~PsmSpecPeptidOms()

pappso::cbor::psm::PsmSpecPeptidOms::~PsmSpecPeptidOms ( )

virtual

Destructor

Definition at line 72 of file psmspecpeptidoms.cpp.

{
}

Member Function Documentation

filterMassSpectrum()

void pappso::cbor::psm::PsmSpecPeptidOms::filterMassSpectrum

(

pappso::MassSpectrum &

mass_spectrum

)

const

Definition at line 88 of file psmspecpeptidoms.cpp.

{
  if(m_deisotope)
    pappso::FilterChargeDeconvolution(m_fragmentTolerance).filter(mass_spectrum);
  pappso::FilterResampleKeepGreater(m_minimumMz).filter(mass_spectrum);
  pappso::FilterGreatestY(m_nMostIntense).filter(mass_spectrum);
}

References pappso::FilterChargeDeconvolution::filter(), pappso::FilterGreatestY::filter(), pappso::FilterResampleKeepGreater::filter(), m_deisotope, m_fragmentTolerance, m_minimumMz, and m_nMostIntense.

getAaCode()

const pappso::AaCode & pappso::cbor::psm::PsmSpecPeptidOms::getAaCode

(

)

const

Definition at line 139 of file psmspecpeptidoms.cpp.

{
  return m_aaCode;
}

References m_aaCode.

newCborScanMap()

pappso::cbor::psm::CborScanMapBase * pappso::cbor::psm::PsmSpecPeptidOms::newCborScanMap ( )

overrideprotectedvirtual

Implements pappso::cbor::psm::PsmFileScanProcess.

Definition at line 133 of file psmspecpeptidoms.cpp.

{
  return new PsmSpecPeptidOmsScan(*this, m_fragmentTolerance);
}

References m_fragmentTolerance, and PsmSpecPeptidOmsScan.

parameterMapReady()

void pappso::cbor::psm::PsmSpecPeptidOms::parameterMapReady ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileScanProcessAndCopy.

Definition at line 120 of file psmspecpeptidoms.cpp.

{
 
  QCborMap cbor_peptidoms_parameters = QCborValue::fromJsonValue(m_specpeptidomsParameters).toMap();
 
  m_cborParameterMap.insert(QString("peptidoms"), cbor_peptidoms_parameters);
 
  mp_cborOutput->append("parameter_map");
  mp_cborOutput->writeCborMap(m_cborParameterMap);
}

References pappso::cbor::psm::PsmFileReaderBase::m_cborParameterMap, m_specpeptidomsParameters, and pappso::cbor::psm::PsmFileScanProcessAndCopy::mp_cborOutput.

processBufferScanDone()

void pappso::cbor::psm::PsmSpecPeptidOms::processBufferScanDone ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileScanProcessAndCopy.

Definition at line 77 of file psmspecpeptidoms.cpp.

{
 
 
  PsmFileScanProcessAndCopy::processBufferScanDone(monitor);
  m_countScanProcessed += m_bufferScanSize;
 
  monitor.setStatus(QObject::tr("%1 scan processed").arg(m_countScanProcessed));
}

References pappso::cbor::psm::PsmFileScanProcess::m_bufferScanSize, m_countScanProcessed, pappso::cbor::psm::PsmFileScanProcessAndCopy::processBufferScanDone(), and pappso::UiMonitorInterface::setStatus().

proteinMapReady()

void pappso::cbor::psm::PsmSpecPeptidOms::proteinMapReady ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileScanProcessAndCopy.

Definition at line 97 of file psmspecpeptidoms.cpp.

{
  if(!m_decoyPrefix.isEmpty())
    {
      // generate decoy sequences
 
      PsmProtein new_decoy_protein;
      for(auto &it_protein : m_proteinMap.getProteinMap())
        {
          new_decoy_protein = it_protein.second;
          new_decoy_protein.protein_sp =
            std::make_shared<Protein>(*new_decoy_protein.protein_sp.get());
          new_decoy_protein.protein_sp.get()->reverse();
          new_decoy_protein.protein_sp.get()->setAccession(
            m_decoyPrefix + new_decoy_protein.protein_sp.get()->getAccession());
          new_decoy_protein.isTarget = false;
        }
    }
  PsmFileScanProcessAndCopy::proteinMapReady(monitor);
}

References pappso::cbor::psm::PsmProtein::isTarget, m_decoyPrefix, pappso::cbor::psm::PsmFileReaderBase::m_proteinMap, pappso::cbor::psm::PsmProtein::protein_sp, and pappso::cbor::psm::PsmFileScanProcessAndCopy::proteinMapReady().

Member Data Documentation

m_aaCode

pappso::AaCode pappso::cbor::psm::PsmSpecPeptidOms::m_aaCode

protected

Definition at line 83 of file psmspecpeptidoms.h.

Referenced by PsmSpecPeptidOms(), and getAaCode().

m_countScanProcessed

std::size_t pappso::cbor::psm::PsmSpecPeptidOms::m_countScanProcessed = 0

protected

Definition at line 92 of file psmspecpeptidoms.h.

Referenced by processBufferScanDone().

m_decoyPrefix

QString pappso::cbor::psm::PsmSpecPeptidOms::m_decoyPrefix

protected

Definition at line 94 of file psmspecpeptidoms.h.

Referenced by proteinMapReady().

m_deisotope

bool pappso::cbor::psm::PsmSpecPeptidOms::m_deisotope = true

protected

Definition at line 88 of file psmspecpeptidoms.h.

Referenced by PsmSpecPeptidOms(), and filterMassSpectrum().

m_fragmentTolerance

pappso::PrecisionPtr pappso::cbor::psm::PsmSpecPeptidOms::m_fragmentTolerance

protected

Definition at line 85 of file psmspecpeptidoms.h.

Referenced by filterMassSpectrum(), and newCborScanMap().

m_maxInterpretationsPerSpectrum

std::size_t pappso::cbor::psm::PsmSpecPeptidOms::m_maxInterpretationsPerSpectrum = 1

protected

Definition at line 95 of file psmspecpeptidoms.h.

Referenced by PsmSpecPeptidOms().

m_minimumMz

double pappso::cbor::psm::PsmSpecPeptidOms::m_minimumMz

protected

Definition at line 86 of file psmspecpeptidoms.h.

Referenced by PsmSpecPeptidOms(), and filterMassSpectrum().

m_newProteinMap

pappso::cbor::psm::PsmProteinMap pappso::cbor::psm::PsmSpecPeptidOms::m_newProteinMap

protected

Definition at line 93 of file psmspecpeptidoms.h.

m_nMostIntense

std::size_t pappso::cbor::psm::PsmSpecPeptidOms::m_nMostIntense

protected

Definition at line 87 of file psmspecpeptidoms.h.

Referenced by PsmSpecPeptidOms(), and filterMassSpectrum().

m_scoreValues

pappso::specpeptidoms::ScoreValues pappso::cbor::psm::PsmSpecPeptidOms::m_scoreValues

protected

Definition at line 89 of file psmspecpeptidoms.h.

m_specpeptidomsParameters

QJsonObject pappso::cbor::psm::PsmSpecPeptidOms::m_specpeptidomsParameters

protected

Definition at line 84 of file psmspecpeptidoms.h.

Referenced by PsmSpecPeptidOms(), and parameterMapReady().

PsmSpecPeptidOmsScan

friend pappso::cbor::psm::PsmSpecPeptidOms::PsmSpecPeptidOmsScan

private

Definition at line 50 of file psmspecpeptidoms.h.

Referenced by newCborScanMap().

---

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