pappso::cbor::psm::PsmFeatures Class Reference

#include <psmfeatures.h>

Inheritance diagram for pappso::cbor::psm::PsmFeatures:

Public Member Functions
	PsmFeatures (std::size_t buffer_scan_size, CborStreamWriter *cbor_output_p)
	PsmFeatures (std::size_t buffer_scan_size, CborStreamWriter *cbor_output_p, const QJsonObject &parameters)
virtual	~PsmFeatures ()
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
Protected Member Functions inherited from pappso::cbor::psm::PsmFileScanProcessAndCopy
void	delayProteinMapInMemory ()
void	informationsReady (pappso::UiMonitorInterface &monitor) override
void	logReady (pappso::UiMonitorInterface &monitor) override
void	parameterMapReady (pappso::UiMonitorInterface &monitor) override
void	fastaFilesReady (pappso::UiMonitorInterface &monitor) override
virtual void	proteinMapReady (pappso::UiMonitorInterface &monitor) override
virtual void	processBufferScanDone (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)

Private Attributes
pappso::XtandemSpectrumProcess	m_tandemSpectrumProcess
double	m_minimumMz = 150
std::list< pappso::Enums::PeptideIon >	m_ionList
pappso::PrecisionPtr	m_fragmentTolerance
pappso::PsmFeatures *	mpa_psmFeatures

Additional Inherited Members
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

Detailed Description

Todo:

write docs

Definition at line 45 of file psmfeatures.h.

Constructor & Destructor Documentation

PsmFeatures() [1/2]

pappso::cbor::psm::PsmFeatures::PsmFeatures	(	std::size_t	buffer_scan_size,
		CborStreamWriter *	cbor_output_p
	)

Default constructor

Definition at line 39 of file psmfeatures.cpp.

  : PsmFileScanProcessAndCopy(buffer_scan_size, cbor_output_p, "psm features")
{
  m_minimumMz = 150;
  m_tandemSpectrumProcess.setMinimumMz(m_minimumMz);
  m_tandemSpectrumProcess.setNmostIntense(100);
  m_tandemSpectrumProcess.setDynamicRange(100);
 
 
  m_ionList.clear();
  m_ionList.push_back(Enums::PeptideIon::y);
  m_ionList.push_back(Enums::PeptideIon::b);
 
  m_fragmentTolerance = pappso::PrecisionFactory::getDaltonInstance(0.02);
 
  mpa_psmFeatures = new pappso::PsmFeatures(m_fragmentTolerance, m_minimumMz);
}

References pappso::Enums::b, pappso::PrecisionFactory::getDaltonInstance(), m_fragmentTolerance, m_ionList, m_minimumMz, m_tandemSpectrumProcess, mpa_psmFeatures, pappso::XtandemSpectrumProcess::setDynamicRange(), pappso::XtandemSpectrumProcess::setMinimumMz(), pappso::XtandemSpectrumProcess::setNmostIntense(), and pappso::Enums::y.

PsmFeatures() [2/2]

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

Definition at line 57 of file psmfeatures.cpp.

  : PsmFileScanProcessAndCopy(buffer_scan_size, cbor_output_p, "psm features")
{
 
  m_ionList.clear();
  m_ionList.push_back(Enums::PeptideIon::y);
  m_ionList.push_back(Enums::PeptideIon::b);
 
  if(parameters.empty())
    {
      m_minimumMz = 150;
      m_tandemSpectrumProcess.setMinimumMz(m_minimumMz);
      m_tandemSpectrumProcess.setNmostIntense(100);
      m_tandemSpectrumProcess.setDynamicRange(100);
      m_fragmentTolerance = pappso::PrecisionFactory::getDaltonInstance(0.02);
    }
  else
    {
 
      m_minimumMz = parameters.value("minimum_mz").toDouble();
      m_tandemSpectrumProcess.setMinimumMz(m_minimumMz);
      m_tandemSpectrumProcess.setNmostIntense(
        parameters.value("hyperscore").toObject().value("n_most_intense").toInt());
      m_tandemSpectrumProcess.setDynamicRange(
        parameters.value("hyperscore").toObject().value("dynamic_range").toInt());
 
 
      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());
        }
    }
 
  mpa_psmFeatures = new pappso::PsmFeatures(m_fragmentTolerance, m_minimumMz);
}

References pappso::Enums::b, pappso::PrecisionFactory::getDaltonInstance(), pappso::PrecisionFactory::getPpmInstance(), m_fragmentTolerance, m_ionList, m_minimumMz, m_tandemSpectrumProcess, mpa_psmFeatures, pappso::XtandemSpectrumProcess::setDynamicRange(), pappso::XtandemSpectrumProcess::setMinimumMz(), pappso::XtandemSpectrumProcess::setNmostIntense(), and pappso::Enums::y.

~PsmFeatures()

pappso::cbor::psm::PsmFeatures::~PsmFeatures ( )

virtual

Destructor

Definition at line 102 of file psmfeatures.cpp.

{
  delete mpa_psmFeatures;
}

References mpa_psmFeatures.

Member Function Documentation

newCborScanMap()

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

overrideprotectedvirtual

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

Definition at line 134 of file psmfeatures.cpp.

{
  return new PsmFeaturesScan(
    *this, m_tandemSpectrumProcess, m_ionList, *mpa_psmFeatures, m_fragmentTolerance);
}

References m_fragmentTolerance, m_ionList, m_tandemSpectrumProcess, and mpa_psmFeatures.

parameterMapReady()

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

overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileReaderBase.

Definition at line 109 of file psmfeatures.cpp.

{
  QCborMap cbor_features_parameters;
 
  cbor_features_parameters.insert(QString("minimum_mz"), m_minimumMz);
  cbor_features_parameters.insert(QString("fragment_tolerance_unit"),
                                  Utils::toString(m_fragmentTolerance->unit()));
  cbor_features_parameters.insert(QString("fragment_tolerance"), m_fragmentTolerance->getNominal());
  cbor_features_parameters.insert(QString("ion_list"), "y b");
 
  QCborMap cbor_hyperscore;
  cbor_hyperscore.insert(QString("minimum_mz"), m_minimumMz);
  cbor_hyperscore.insert(QString("n_most_intense"), m_tandemSpectrumProcess.getNmostIntense());
  cbor_hyperscore.insert(QString("dynamic_range"), m_tandemSpectrumProcess.getDynamicRange());
 
  cbor_features_parameters.insert(QString("hyperscore"), cbor_hyperscore);
 
  m_cborParameterMap.insert(QString("features"), cbor_features_parameters);
 
  mp_cborOutput->append("parameter_map");
  mp_cborOutput->writeCborMap(m_cborParameterMap);
}

References pappso::XtandemSpectrumProcess::getDynamicRange(), pappso::XtandemSpectrumProcess::getNmostIntense(), pappso::PrecisionBase::getNominal(), pappso::cbor::psm::PsmFileReaderBase::m_cborParameterMap, m_fragmentTolerance, m_minimumMz, m_tandemSpectrumProcess, pappso::cbor::psm::PsmFileScanProcessAndCopy::mp_cborOutput, pappso::Utils::toString(), pappso::PrecisionBase::unit(), and pappso::cbor::CborStreamWriter::writeCborMap().

Member Data Documentation

m_fragmentTolerance

pappso::PrecisionPtr pappso::cbor::psm::PsmFeatures::m_fragmentTolerance

private

Definition at line 72 of file psmfeatures.h.

Referenced by PsmFeatures(), PsmFeatures(), newCborScanMap(), and parameterMapReady().

m_ionList

std::list<pappso::Enums::PeptideIon> pappso::cbor::psm::PsmFeatures::m_ionList

private

Definition at line 71 of file psmfeatures.h.

Referenced by PsmFeatures(), PsmFeatures(), and newCborScanMap().

m_minimumMz

double pappso::cbor::psm::PsmFeatures::m_minimumMz = 150

private

Definition at line 70 of file psmfeatures.h.

Referenced by PsmFeatures(), PsmFeatures(), and parameterMapReady().

m_tandemSpectrumProcess

pappso::XtandemSpectrumProcess pappso::cbor::psm::PsmFeatures::m_tandemSpectrumProcess

private

Definition at line 69 of file psmfeatures.h.

Referenced by PsmFeatures(), PsmFeatures(), newCborScanMap(), and parameterMapReady().

mpa_psmFeatures

pappso::PsmFeatures* pappso::cbor::psm::PsmFeatures::mpa_psmFeatures

private

Definition at line 73 of file psmfeatures.h.

Referenced by PsmFeatures(), PsmFeatures(), ~PsmFeatures(), and newCborScanMap().

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

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