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
	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
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)
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
	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
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

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

Definition at line 48 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();
  mp_copyCborOutput = nullptr;
}

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

Referenced by pappso::cbor::psm::PsmFeatures::PsmFeatures(), pappso::cbor::psm::PsmFeatures::PsmFeatures(), pappso::cbor::psm::PsmIonSeries::PsmIonSeries(), 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 55 of file psmfilescanprocessandcopy.cpp.

{
  if(mpa_bufferAfterProteinMap != nullptr)
    {
      delete mpa_bufferAfterProteinMap;
    }
  if(mpa_bufferWriterAfterProteinMap != nullptr)
    {
      delete mpa_bufferWriterAfterProteinMap;
    }
}

References mpa_bufferAfterProteinMap, and mpa_bufferWriterAfterProteinMap.

Member Function Documentation

◆ close()

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

overridevirtual

convenient function to clean pointer before leaving

Reimplemented from pappso::cbor::CborStreamReaderInterface.

Definition at line 79 of file psmfilescanprocessandcopy.cpp.

{
  if(mp_copyCborOutput == nullptr)
    {
      mp_cborOutput->endMap();
    }
  else
    {
 
      // mpa_bufferWriterAfterProteinMap->endArray(); // end scan_list
      // mpa_bufferWriterAfterProteinMap->endMap();   // end sample
      // mpa_bufferWriterAfterProteinMap->endArray(); // end sample_list
 
      mp_copyCborOutput->append("protein_map");
      m_psmNewProteinMap.writeMap(*mp_copyCborOutput);
 
      // copy buffer
 
      mp_copyCborOutput->append("sample_list");
 
      // mpa_writer->startArray(); // sample_list
      // mpa_writer->endArray();   // end sample_list
 
 
      mpa_bufferAfterProteinMap->seek(0);
      // qWarning() << "size=" << mpa_buffer->data().size();
 
      mp_copyCborOutput->device()->write(mpa_bufferAfterProteinMap->data());
 
      mp_copyCborOutput->endMap();
    }
}

References m_psmNewProteinMap, mp_cborOutput, mp_copyCborOutput, and mpa_bufferAfterProteinMap.

◆ delayProteinMapInMemory()

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

protected

Definition at line 69 of file psmfilescanprocessandcopy.cpp.

{
  mp_copyCborOutput = mp_cborOutput;
 
  mpa_bufferAfterProteinMap = new QBuffer();
  mpa_bufferAfterProteinMap->open(QIODevice::ReadWrite);
  mpa_bufferWriterAfterProteinMap = new pappso::cbor::CborStreamWriter(mpa_bufferAfterProteinMap);
}

References mp_cborOutput, mp_copyCborOutput, mpa_bufferAfterProteinMap, and mpa_bufferWriterAfterProteinMap.

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

◆ fastaFilesReady()

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

overrideprotectedvirtual

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

Definition at line 135 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 113 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 120 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::PsmIonSeries, pappso::cbor::psm::PsmNewEval, pappso::cbor::psm::PsmSpecGlob, and pappso::cbor::psm::PsmSpecPeptidOms.

Definition at line 128 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.

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

Definition at line 169 of file psmfilescanprocessandcopy.cpp.

{
 
  // monitor.setStatus(QObject::tr("PsmFileScanProcessAndCopy::processBufferScanDone"));
  for(CborScanMapBase *cbor_scan_p : m_cborScanList)
    {
      // qDebug() << cbor_scan_p->keys();
      cbor_scan_p->filterAndSortPsmList();
 
      if(mp_copyCborOutput != nullptr)
        {
          // populate new protein map
          cbor_scan_p->populateProteinMapUsingOldProteinMap(m_proteinMap, m_psmNewProteinMap);
        }
 
 
      // qWarning() << "PsmFileScanProcessAndCopy::processBufferScanDone "
      //           << cbor_scan_p->value("psm_list").toArray().size();
 
      // cbor_scan_p->write(*mp_cborOutput);
      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, pappso::cbor::psm::PsmFileReaderBase::m_proteinMap, m_psmNewProteinMap, mp_cborOutput, and mp_copyCborOutput.

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

◆ proteinMapReady()

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

overrideprotectedvirtual

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

Reimplemented in pappso::cbor::psm::PsmSpecPeptidOms.

Definition at line 153 of file psmfilescanprocessandcopy.cpp.

{
  if(mp_copyCborOutput == nullptr)
    {
      mp_cborOutput->append("protein_map");
      m_proteinMap.writeMap(*mp_cborOutput);
    }
  else
    {
      // protein map writing is delayed : swap to temporary buffer writer
      mp_cborOutput = mpa_bufferWriterAfterProteinMap;
    }
}

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

Referenced by pappso::cbor::psm::PsmSpecPeptidOms::proteinMapReady().

◆ sampleFinished()

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

overrideprotectedvirtual

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

Definition at line 219 of file psmfilescanprocessandcopy.cpp.

{
 
  processBufferScan(monitor);
  clearScanBuffer();
 
  mp_cborOutput->endArray();
  mp_cborOutput->endMap();
}

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

◆ sampleListFinished()

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

overrideprotectedvirtual

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

Definition at line 240 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 230 of file psmfilescanprocessandcopy.cpp.

{
  if(mp_copyCborOutput == nullptr)
    {
      mp_cborOutput->append("sample_list");
    }
  mp_cborOutput->startArray();
}

References mp_cborOutput, and mp_copyCborOutput.

◆ sampleStarted()

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

overrideprotectedvirtual

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

Definition at line 201 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();
}