Basic PSM file reader to process scan (parallelized scan processing) and write a new resulting PSM file. More...

#include <psmfilescanprocessandcopy.h>

Inheritance diagram for pappso::cbor::psm::PsmFileScanProcessAndCopy:

Public Member Functions
	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
void	informationsReady (pappso::UiMonitorInterface &monitor) override

void	logReady (pappso::UiMonitorInterface &monitor) override

void	parameterMapReady (pappso::UiMonitorInterface &monitor) override

void	fastaFilesReady (pappso::UiMonitorInterface &monitor) override

void	proteinMapReady (pappso::UiMonitorInterface &monitor) override

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)

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	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
CborStreamWriter *	mp_cborOutput

QString	m_operation

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

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

Basic PSM file reader to process scan (parallelized scan processing) and write a new resulting PSM file.

Definition at line 45 of file psmfilescanprocessandcopy.h.

Constructor & Destructor Documentation

◆ PsmFileScanProcessAndCopy()

pappso::cbor::psm::PsmFileScanProcessAndCopy::PsmFileScanProcessAndCopy	(	std::size_t	buffer_scan_size,
		CborStreamWriter *	cbor_output_p,
		const QString &	operation )

Default constructor

Definition at line 41 of file psmfilescanprocessandcopy.cpp.

  : PsmFileScanProcess(buffer_scan_size)
{
  mp_cborOutput = cbor_output_p;
  m_operation   = operation;
 
 
  mp_cborOutput->startMap();
}

References pappso::cbor::psm::PsmFileScanProcess::PsmFileScanProcess(), m_operation, and mp_cborOutput.

Referenced by pappso::cbor::psm::PsmFeatures::PsmFeatures(), pappso::cbor::psm::PsmFeatures::PsmFeatures(), pappso::cbor::psm::PsmNewEval::PsmNewEval(), pappso::cbor::psm::PsmSpecGlob::PsmSpecGlob(), and pappso::cbor::psm::PsmSpecPeptidOms::PsmSpecPeptidOms().

◆ ~PsmFileScanProcessAndCopy()

pappso::cbor::psm::PsmFileScanProcessAndCopy::~PsmFileScanProcessAndCopy ( )

virtual

Destructor

Definition at line 53 of file psmfilescanprocessandcopy.cpp.

54{

55}

Member Function Documentation

◆ close()

void pappso::cbor::psm::PsmFileScanProcessAndCopy::close ( )

overridevirtual

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

Definition at line 58 of file psmfilescanprocessandcopy.cpp.

{
  mp_cborOutput->endMap();
}

References mp_cborOutput.

◆ fastaFilesReady()

void pappso::cbor::psm::PsmFileScanProcessAndCopy::fastaFilesReady ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 86 of file psmfilescanprocessandcopy.cpp.

{
  // "target_fasta_files": ["zea_mays.fasta", "contaminant.fasta"],
  if(!m_targetFastaFiles.isEmpty())
    {
      mp_cborOutput->append("target_fasta_files");
      mp_cborOutput->writeArray(m_targetFastaFiles);
    }
  //"decoy_fasta_files" : ["rev_zea_mays.fasta", "rev_contaminant.fasta"],
 
  if(!m_decoyFastaFiles.isEmpty())
    {
      mp_cborOutput->append("decoy_fasta_files");
      mp_cborOutput->writeArray(m_decoyFastaFiles);
    }
}

References pappso::cbor::psm::PsmFileReaderBase::m_decoyFastaFiles, pappso::cbor::psm::PsmFileReaderBase::m_targetFastaFiles, and mp_cborOutput.

◆ informationsReady()

void pappso::cbor::psm::PsmFileScanProcessAndCopy::informationsReady ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 64 of file psmfilescanprocessandcopy.cpp.

{
  mp_cborOutput->writeInformations("pappsomspp_copy", Utils::getVersion(), "psm", m_operation);
}

References pappso::Utils::getVersion(), m_operation, and mp_cborOutput.

◆ logReady()

void pappso::cbor::psm::PsmFileScanProcessAndCopy::logReady ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 71 of file psmfilescanprocessandcopy.cpp.

{
  m_cborLog.append(m_cborInformations);
  mp_cborOutput->append("log");
  mp_cborOutput->writeCborArray(m_cborLog);
}

References pappso::cbor::psm::PsmFileReaderBase::m_cborInformations, pappso::cbor::psm::PsmFileReaderBase::m_cborLog, and mp_cborOutput.

◆ parameterMapReady()

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

overrideprotectedvirtual

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

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

Definition at line 79 of file psmfilescanprocessandcopy.cpp.

{
  mp_cborOutput->append("parameter_map");
  mp_cborOutput->writeCborMap(m_cborParameterMap);
}

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

◆ processBufferScanDone()

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

overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileScanProcess.

Definition at line 113 of file psmfilescanprocessandcopy.cpp.

{
  for(const CborScanMapBase *cbor_scan_p : m_cborScanList)
    {
      // qDebug() << cbor_scan_p->keys();
 
 
      mp_cborOutput->writeCborMap(*cbor_scan_p);
 
      if(!cbor_scan_p->keys().contains("id"))
        {
          throw pappso::PappsoException(
            QObject::tr("missing scan id %1").arg(cbor_scan_p->keys().size()));
        }
    }
}

References pappso::cbor::psm::PsmFileScanProcess::CborScanMapBase, pappso::cbor::psm::PsmFileScanProcess::m_cborScanList, and mp_cborOutput.

◆ proteinMapReady()

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

overrideprotectedvirtual

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

Definition at line 104 of file psmfilescanprocessandcopy.cpp.

{
 
  mp_cborOutput->append("protein_map");
  m_proteinMap.writeMap(*mp_cborOutput);
}

References pappso::cbor::psm::PsmFileReaderBase::m_proteinMap, and mp_cborOutput.

◆ sampleFinished()

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

overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileScanProcess.

Definition at line 151 of file psmfilescanprocessandcopy.cpp.

{
 
  mp_cborOutput->endArray();
  mp_cborOutput->endMap();
}

References mp_cborOutput.

◆ sampleListFinished()

void pappso::cbor::psm::PsmFileScanProcessAndCopy::sampleListFinished ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 168 of file psmfilescanprocessandcopy.cpp.

{
  mp_cborOutput->endArray();
}

References mp_cborOutput.

◆ sampleListStarted()

void pappso::cbor::psm::PsmFileScanProcessAndCopy::sampleListStarted ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 160 of file psmfilescanprocessandcopy.cpp.

{
  mp_cborOutput->append("sample_list");
  mp_cborOutput->startArray();
}

References mp_cborOutput.

◆ sampleStarted()

void pappso::cbor::psm::PsmFileScanProcessAndCopy::sampleStarted ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 132 of file psmfilescanprocessandcopy.cpp.

{
  mp_cborOutput->startMap();
  mp_cborOutput->append("name");
  mp_cborOutput->append(m_currentSampleName);
  if(m_currentIdentificationFileList.size() > 0)
    {
      mp_cborOutput->append("identification_file_list");
      writePsmFileList(*mp_cborOutput, m_currentIdentificationFileList);
    }
  mp_cborOutput->append("peaklist_file");
  writePsmFile(*mp_cborOutput, m_currentPeaklistFile);
 
  mp_cborOutput->append("scan_list");
  mp_cborOutput->startArray();
}

References pappso::cbor::psm::PsmFileReaderBase::m_currentIdentificationFileList, pappso::cbor::psm::PsmFileReaderBase::m_currentPeaklistFile, pappso::cbor::psm::PsmFileReaderBase::m_currentSampleName, mp_cborOutput, pappso::cbor::psm::PsmFileReaderBase::writePsmFile(), and pappso::cbor::psm::PsmFileReaderBase::writePsmFileList().

Member Data Documentation

◆ m_operation

QString pappso::cbor::psm::PsmFileScanProcessAndCopy::m_operation

protected

Definition at line 82 of file psmfilescanprocessandcopy.h.

Referenced by PsmFileScanProcessAndCopy(), and informationsReady().

◆ mp_cborOutput

CborStreamWriter* pappso::cbor::psm::PsmFileScanProcessAndCopy::mp_cborOutput

protected

Definition at line 81 of file psmfilescanprocessandcopy.h.

Referenced by PsmFileScanProcessAndCopy(), close(), fastaFilesReady(), informationsReady(), logReady(), pappso::cbor::psm::PsmFeatures::parameterMapReady(), parameterMapReady(), pappso::cbor::psm::PsmNewEval::parameterMapReady(), pappso::cbor::psm::PsmSpecGlob::parameterMapReady(), processBufferScanDone(), proteinMapReady(), sampleFinished(), sampleListFinished(), sampleListStarted(), and sampleStarted().

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

pappsomspp/core/processing/cbor/psm/psmfilescanprocessandcopy.h
pappsomspp/core/processing/cbor/psm/psmfilescanprocessandcopy.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PsmFileScanProcessAndCopy()

◆ ~PsmFileScanProcessAndCopy()

Member Function Documentation

◆ close()

◆ fastaFilesReady()

◆ informationsReady()

◆ logReady()

◆ parameterMapReady()

◆ processBufferScanDone()

◆ proteinMapReady()

◆ sampleFinished()

◆ sampleListFinished()

◆ sampleListStarted()

◆ sampleStarted()

Member Data Documentation

◆ m_operation

◆ mp_cborOutput