pappso::cbor::psm::PsmFileScanProcess Class Reference

Basic PSM file reader to process scan (parallelized scan processing). More...

#include <psmfilescanprocess.h>

Inheritance diagram for pappso::cbor::psm::PsmFileScanProcess:

Public Member Functions
	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 ()
virtual void	close ()
	convenient function to clean pointer before leaving

Protected Member Functions
void	readScan (pappso::UiMonitorInterface &monitor) override
void	scanFinished (pappso::UiMonitorInterface &monitor) override
void	sampleFinished (pappso::UiMonitorInterface &monitor) override
virtual void	processBufferScan (pappso::UiMonitorInterface &monitor)
virtual void	processBufferScanDone (pappso::UiMonitorInterface &monitor)
virtual CborScanMapBase *	newCborScanMap ()=0
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	logReady (pappso::UiMonitorInterface &monitor)
virtual void	informationsReady (pappso::UiMonitorInterface &monitor)
virtual void	parameterMapReady (pappso::UiMonitorInterface &monitor)
virtual void	fastaFilesReady (pappso::UiMonitorInterface &monitor)
virtual void	proteinMapReady (pappso::UiMonitorInterface &monitor)
virtual void	sampleListStarted (pappso::UiMonitorInterface &monitor)
virtual void	sampleStarted (pappso::UiMonitorInterface &monitor)
virtual void	scanStarted (pappso::UiMonitorInterface &monitor)
virtual void	sampleListFinished (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
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	CborScanMapBase

Detailed Description

Basic PSM file reader to process scan (parallelized scan processing).

Definition at line 46 of file psmfilescanprocess.h.

Constructor & Destructor Documentation

PsmFileScanProcess()

pappso::cbor::psm::PsmFileScanProcess::PsmFileScanProcess

(

std::size_t

buffer_scan_size

)

Default constructor

Definition at line 41 of file psmfilescanprocess.cpp.

{
  m_bufferScanSize = buffer_scan_size;
}

References m_bufferScanSize.

Referenced by pappso::cbor::psm::PsmFileScanProcessAndCopy::PsmFileScanProcessAndCopy().

~PsmFileScanProcess()

pappso::cbor::psm::PsmFileScanProcess::~PsmFileScanProcess ( )

virtual

Destructor

Definition at line 46 of file psmfilescanprocess.cpp.

{
}

Member Function Documentation

clearScanBuffer()

void pappso::cbor::psm::PsmFileScanProcess::clearScanBuffer ( )

protected

Definition at line 51 of file psmfilescanprocess.cpp.

{
  for(CborScanMapBase *cbor_scan_p : m_cborScanList)
    {
      delete cbor_scan_p;
    }
  m_cborScanList.clear();
}

References CborScanMapBase, and m_cborScanList.

Referenced by newCborScanMap(), sampleFinished(), pappso::cbor::psm::PsmFileScanProcessAndCopy::sampleFinished(), and scanFinished().

newCborScanMap()

virtual CborScanMapBase * pappso::cbor::psm::PsmFileScanProcess::newCborScanMap ( )

protectedpure virtual

Implemented in pappso::cbor::psm::PsmFeatures, pappso::cbor::psm::PsmIonSeries, pappso::cbor::psm::PsmNewEval, pappso::cbor::psm::PsmSpecGlob, and pappso::cbor::psm::PsmSpecPeptidOms.

References CborScanMapBase, and clearScanBuffer().

Referenced by readScan().

processBufferScan()

void pappso::cbor::psm::PsmFileScanProcess::processBufferScan ( pappso::UiMonitorInterface & monitor )

protectedvirtual

Definition at line 102 of file psmfilescanprocess.cpp.

{
  // you decide how to process the list of scans
  // monitor.setStatus(
  //  QObject::tr("PsmFileScanProcess::processBufferScan %1").arg(m_cborScanList.size()));
  std::function<void(CborScanMapBase *)> mapProcessCborScan = [](CborScanMapBase *cbor_scan_p) {
    cbor_scan_p->process();
  };
 
 
  QFuture<void> res = QtConcurrent::map<std::vector<CborScanMapBase *>::iterator>(
    m_cborScanList.begin(), m_cborScanList.end(), mapProcessCborScan);
  res.waitForFinished();
  processBufferScanDone(monitor);
 
  // monitor.setStatus(
  //  QObject::tr("PsmFileScanProcess::processBufferScan %1 done").arg(m_cborScanList.size()));
}

References CborScanMapBase, m_cborScanList, and processBufferScanDone().

Referenced by sampleFinished(), pappso::cbor::psm::PsmFileScanProcessAndCopy::sampleFinished(), and scanFinished().

processBufferScanDone()

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

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmFileScanProcessAndCopy, pappso::cbor::psm::PsmSpecGlob, and pappso::cbor::psm::PsmSpecPeptidOms.

Definition at line 122 of file psmfilescanprocess.cpp.

{
  // you decide what to do with processed scans
}

Referenced by processBufferScan().

readScan()

void pappso::cbor::psm::PsmFileScanProcess::readScan ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 62 of file psmfilescanprocess.cpp.

{
  qDebug();
  //  auto& ref = elections.emplace_back("Nelson Mandela", "South Africa", 1994);
  CborScanMapBase *scan_map_p = newCborScanMap();
  m_cborScanList.push_back(scan_map_p);
 
  if(!mpa_cborReader->readCborMap(*scan_map_p))
    {
      throw pappso::PappsoException(QObject::tr("readCborMap scan failed"));
    }
  // m_cborScanList.push_back(scan_map);
  qDebug() << "scan end";
  scanFinished(monitor);
  qDebug();
}

References CborScanMapBase, m_cborScanList, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, newCborScanMap(), and scanFinished().

sampleFinished()

void pappso::cbor::psm::PsmFileScanProcess::sampleFinished ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Reimplemented in pappso::cbor::psm::PsmFileScanProcessAndCopy.

Definition at line 93 of file psmfilescanprocess.cpp.

{
  // qWarning() << "sampleFinished";
  processBufferScan(monitor);
  clearScanBuffer();
}

References clearScanBuffer(), and processBufferScan().

scanFinished()

void pappso::cbor::psm::PsmFileScanProcess::scanFinished ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 80 of file psmfilescanprocess.cpp.

{
 
  // monitor.setStatus(QObject::tr("PsmFileScanProcess::scanFinished
  // %1").arg(m_cborScanList.size()));
  if(m_cborScanList.size() > m_bufferScanSize)
    {
      processBufferScan(monitor);
      clearScanBuffer();
    }
}

References clearScanBuffer(), m_bufferScanSize, m_cborScanList, and processBufferScan().

Referenced by readScan().

Member Data Documentation

CborScanMapBase

friend pappso::cbor::psm::PsmFileScanProcess::CborScanMapBase

private

Definition at line 49 of file psmfilescanprocess.h.

Referenced by clearScanBuffer(), newCborScanMap(), processBufferScan(), pappso::cbor::psm::PsmFileScanProcessAndCopy::processBufferScanDone(), and readScan().

m_bufferScanSize

std::size_t pappso::cbor::psm::PsmFileScanProcess::m_bufferScanSize = 1000

protected

Definition at line 73 of file psmfilescanprocess.h.

Referenced by PsmFileScanProcess(), pappso::cbor::psm::PsmSpecGlob::processBufferScanDone(), pappso::cbor::psm::PsmSpecPeptidOms::processBufferScanDone(), and scanFinished().

m_cborScanList

std::vector<CborScanMapBase *> pappso::cbor::psm::PsmFileScanProcess::m_cborScanList

protected

Definition at line 74 of file psmfilescanprocess.h.

Referenced by clearScanBuffer(), processBufferScan(), pappso::cbor::psm::PsmFileScanProcessAndCopy::processBufferScanDone(), readScan(), and scanFinished().

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

• pappsomspp/core/processing/cbor/psm/psmfilescanprocess.h
• pappsomspp/core/processing/cbor/psm/psmfilescanprocess.cpp