computes spectrum isotope match for each PSM and stores ion series in "props" More...

#include <psmionseries.h>

Inheritance diagram for pappso::cbor::psm::PsmIonSeries:

Public Member Functions
	PsmIonSeries (std::size_t buffer_scan_size, CborStreamWriter *cbor_output_p, const QJsonObject &parameters)

virtual	~PsmIonSeries ()

void	filterMassSpectrum (pappso::MassSpectrum &mass_spectrum) 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

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 ()

void	readCbor (QFile *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	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

bool	currentProteinRefListContainsDecoy () const

bool	currentProteinRefListContainsTarget () const

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)

Protected Attributes
QJsonObject	m_psmIonSeriesParameters

pappso::PrecisionPtr	m_fragmentTolerance

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_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

computes spectrum isotope match for each PSM and stores ion series in "props"

Definition at line 43 of file psmionseries.h.

Constructor & Destructor Documentation

◆ PsmIonSeries()

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

Default constructor

Definition at line 35 of file psmionseries.cpp.

  : PsmFileScanProcessAndCopy(buffer_scan_size, cbor_output_p, "IonSeries")
{
  m_psmIonSeriesParameters = 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());
    }
}

References pappso::PrecisionFactory::getDaltonInstance(), pappso::PrecisionFactory::getPpmInstance(), m_fragmentTolerance, and m_psmIonSeriesParameters.

◆ ~PsmIonSeries()

pappso::cbor::psm::PsmIonSeries::~PsmIonSeries ( )

virtual

Destructor

Definition at line 54 of file psmionseries.cpp.

55{

56}

Member Function Documentation

◆ filterMassSpectrum()

void pappso::cbor::psm::PsmIonSeries::filterMassSpectrum ( pappso::MassSpectrum & mass_spectrum ) const

◆ newCborScanMap()

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

overrideprotectedvirtual

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

Definition at line 78 of file psmionseries.cpp.

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

◆ parameterMapReady()

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

overrideprotectedvirtual

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

Definition at line 59 of file psmionseries.cpp.

{
  QCborMap cbor_features_parameters;
 
  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");
 
 
  m_cborParameterMap.insert(QString("ion-series"), cbor_features_parameters);
 
  mp_cborOutput->append("parameter_map");
  mp_cborOutput->writeCborMap(m_cborParameterMap);
}

References pappso::Utils::toString().

Member Data Documentation

◆ m_fragmentTolerance

pappso::PrecisionPtr pappso::cbor::psm::PsmIonSeries::m_fragmentTolerance

protected

Definition at line 67 of file psmionseries.h.

Referenced by PsmIonSeries().

◆ m_psmIonSeriesParameters

QJsonObject pappso::cbor::psm::PsmIonSeries::m_psmIonSeriesParameters