#include <psmneweval.h>

Inheritance diagram for pappso::cbor::psm::PsmNewEval:

Public Member Functions
	PsmNewEval (std::size_t buffer_scan_size, CborStreamWriter *cbor_output_p, const QString &eval_name, const QJsonObject &parameters)
virtual	~PsmNewEval ()
void	addEvalDoubleVector (const QString &eval_key_value_name, std::vector< double > arr_values)
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
pappso::cbor::psm::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
	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
QJsonObject	m_newEvalParameters
QString	m_evalName
QString	m_evalKeyValueName
std::vector< double >	m_psmEvalValues
std::vector< double >::iterator	value_it
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 37 of file psmneweval.h.

Constructor & Destructor Documentation

◆ PsmNewEval()

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

Default constructor

Definition at line 31 of file psmneweval.cpp.

  : PsmFileScanProcessAndCopy(buffer_scan_size, cbor_output_p, QString("add %1").append(eval_name))
{
  qDebug();
  m_newEvalParameters = parameters;
  m_evalName          = eval_name;
  qDebug();
}

References pappso::cbor::psm::PsmFileScanProcessAndCopy::PsmFileScanProcessAndCopy(), m_evalName, and m_newEvalParameters.

◆ ~PsmNewEval()

pappso::cbor::psm::PsmNewEval::~PsmNewEval ( )

virtual

Definition at line 43 of file psmneweval.cpp.

44{

45}

Member Function Documentation

◆ addEvalDoubleVector()

void pappso::cbor::psm::PsmNewEval::addEvalDoubleVector	(	const QString &	eval_key_value_name,
		std::vector< double >	arr_values )

Definition at line 57 of file psmneweval.cpp.

{
  m_evalKeyValueName = eval_key_value_name;
  m_psmEvalValues    = arr_values;
}

References m_evalKeyValueName, and m_psmEvalValues.

◆ newCborScanMap()

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

overrideprotectedvirtual

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

Definition at line 48 of file psmneweval.cpp.

{
  CborScanMapBase *p_cbor_scan_map = new CborScanMapBase(*this);
  value_it                         = p_cbor_scan_map->addPsmEvalVectorDouble(
    m_evalName, m_evalKeyValueName, value_it, m_psmEvalValues.end());
  return p_cbor_scan_map;
}

References pappso::cbor::psm::CborScanMapBase::addPsmEvalVectorDouble(), m_evalKeyValueName, m_evalName, m_psmEvalValues, and value_it.

◆ parameterMapReady()

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

overrideprotectedvirtual

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

Definition at line 65 of file psmneweval.cpp.

{
  qDebug();
  QCborMap cbor_neweval_parameters = QCborValue::fromJsonValue(m_newEvalParameters).toMap();
 
 
  m_cborParameterMap.insert(m_evalName, cbor_neweval_parameters);
 
 
  mp_cborOutput->append("parameter_map");
  mp_cborOutput->writeCborMap(m_cborParameterMap);
  qDebug();
}

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

Member Data Documentation

◆ m_evalKeyValueName

QString pappso::cbor::psm::PsmNewEval::m_evalKeyValueName

protected

Definition at line 59 of file psmneweval.h.

Referenced by addEvalDoubleVector(), and newCborScanMap().

◆ m_evalName

QString pappso::cbor::psm::PsmNewEval::m_evalName

protected

Definition at line 58 of file psmneweval.h.

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

◆ m_newEvalParameters

QJsonObject pappso::cbor::psm::PsmNewEval::m_newEvalParameters

protected

Definition at line 57 of file psmneweval.h.

Referenced by PsmNewEval(), and parameterMapReady().

◆ m_psmEvalValues

std::vector<double> pappso::cbor::psm::PsmNewEval::m_psmEvalValues

protected

Definition at line 60 of file psmneweval.h.

Referenced by addEvalDoubleVector(), and newCborScanMap().

◆ value_it

std::vector<double>::iterator pappso::cbor::psm::PsmNewEval::value_it

protected

Definition at line 62 of file psmneweval.h.

Referenced by newCborScanMap().

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

pappsomspp/core/processing/cbor/psm/evalscan/psmneweval.h
pappsomspp/core/processing/cbor/psm/evalscan/psmneweval.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PsmNewEval()

◆ ~PsmNewEval()

Member Function Documentation

◆ addEvalDoubleVector()

◆ newCborScanMap()

◆ parameterMapReady()

Member Data Documentation

◆ m_evalKeyValueName

◆ m_evalName

◆ m_newEvalParameters

◆ m_psmEvalValues

◆ value_it