#include <psmfilereaderbase.h>

Inheritance diagram for pappso::cbor::psm::PsmFileReaderBase:

Classes
struct	PsmProteinRef

Public Member Functions
	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	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	readScan (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	scanFinished (pappso::UiMonitorInterface &monitor)
virtual void	sampleFinished (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
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 55 of file psmfilereaderbase.h.

Constructor & Destructor Documentation

◆ PsmFileReaderBase()

pappso::cbor::psm::PsmFileReaderBase::PsmFileReaderBase ( )

Default constructor

Definition at line 44 of file psmfilereaderbase.cpp.

                                     : CborStreamReaderInterface()
{
}

References pappso::cbor::CborStreamReaderInterface::CborStreamReaderInterface().

◆ ~PsmFileReaderBase()

pappso::cbor::psm::PsmFileReaderBase::~PsmFileReaderBase ( )

overridevirtual

Destructor

Definition at line 48 of file psmfilereaderbase.cpp.

{
  // qWarning() << "~PsmFileReaderBase";
}

Member Function Documentation

◆ currentProteinRefListContainsDecoy()

bool pappso::cbor::psm::PsmFileReaderBase::currentProteinRefListContainsDecoy ( ) const

protected

tells if the current PSM has a decoy accession

Returns: boolean

Definition at line 85 of file psmfilereaderbase.cpp.

{
  for(auto &it : m_currentPsmProteinRefList)
    {
      if(!m_proteinMap.getByAccession(it.accession).isTarget)
        return true;
    }
  return false;
}

References m_currentPsmProteinRefList, and m_proteinMap.

◆ currentProteinRefListContainsTarget()

bool pappso::cbor::psm::PsmFileReaderBase::currentProteinRefListContainsTarget ( ) const

protected

tells if the current PSM has a target accession

Returns: boolean

Definition at line 96 of file psmfilereaderbase.cpp.

{
  for(auto &it : m_currentPsmProteinRefList)
    {
      if(m_proteinMap.getByAccession(it.accession).isTarget)
        return true;
    }
  return false;
}

References m_currentPsmProteinRefList, and m_proteinMap.

◆ fastaFilesReady()

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

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmCbor2Json, pappso::cbor::psm::PsmFileAppend, and pappso::cbor::psm::PsmFileScanProcessAndCopy.

Definition at line 700 of file psmfilereaderbase.cpp.

701{

702}

Referenced by readRoot().

◆ getCurrentPsmPeptideSp()

pappso::PeptideSp pappso::cbor::psm::PsmFileReaderBase::getCurrentPsmPeptideSp ( ) const

protected

Definition at line 730 of file psmfilereaderbase.cpp.

{
  pappso::PeptideSp peptide_sp;
  if(m_currentPsmProforma.isEmpty())
    {
      throw pappso::PappsoException(QObject::tr("ERROR: m_currentPsmProforma is empty"));
    }
  else
    {
      peptide_sp = pappso::PeptideProFormaParser::parseString(m_currentPsmProforma);
    }
  return peptide_sp;
}

References m_currentPsmProforma, and pappso::PeptideProFormaParser::parseString().

◆ getCurrentQualifiedMassSpectrumSPtr()

pappso::QualifiedMassSpectrumSPtr pappso::cbor::psm::PsmFileReaderBase::getCurrentQualifiedMassSpectrumSPtr ( ) const

protected

get the qualified Spectrum for the current PSM

Returns: a qualified mass spectrum

Definition at line 745 of file psmfilereaderbase.cpp.

{
  if(m_currentPeaklistFile.name.isEmpty())
    {
      throw pappso::PappsoException(QObject::tr("ERROR: m_currentPeaklistFile is empty"));
    }
  if(m_cborScanId.isEmpty())
    {
      throw pappso::PappsoException(QObject::tr("ERROR: m_cborScanId is empty"));
    }
  if(m_cborScanPrecursor.isEmpty())
    {
      throw pappso::PappsoException(QObject::tr("ERROR: m_cborScanPrecursor is empty"));
    }
 
  if(!m_cborScanId.keys().contains("index"))
    {
      throw pappso::PappsoException("There is no scan index");
    }
 
  if(m_cborScanMs2.isEmpty())
    {
      throw pappso::PappsoException(QObject::tr("ERROR: m_cborScanMs2 is empty"));
    }
  else
    {
      if(!m_cborScanMs2.keys().contains("mz"))
        {
          throw pappso::PappsoException("There is no ms2 mz values");
        }
      if(!m_cborScanMs2.keys().contains("intensity"))
        {
          throw pappso::PappsoException("There is no ms2 intensity values");
        }
    }
  pappso::MsRunId msrun_id(m_currentPeaklistFile.name);
  msrun_id.setSampleName(m_currentSampleName);
  pappso::MsRunIdCstSPtr msrun_id_sp = std::make_shared<const pappso::MsRunId>(msrun_id);
  pappso::MassSpectrumId ms_id(msrun_id_sp);
  ms_id.setSpectrumIndex(m_cborScanId.value("index").toInteger());
 
  // native_id
  if(m_cborScanId.keys().contains("native_id"))
    {
      ms_id.setNativeId(m_cborScanId.value("native_id").toString());
    }
 
  std::vector<DataPoint> data_point_vector;
  std::size_t i = 0;
  for(auto cbor_mz_value : m_cborScanMs2.value("mz").toArray())
    {
      data_point_vector.push_back(
        {cbor_mz_value.toDouble(), m_cborScanMs2.value("intensity").toArray().at(i).toDouble()});
      i++;
    }
 
 
  MassSpectrum mass_spectrum(data_point_vector);
  pappso::PrecursorIonData precursor_ion_data;
 
  pappso::QualifiedMassSpectrum qualified_mass_spectrum(ms_id);
  qualified_mass_spectrum.setMassSpectrumSPtr(mass_spectrum.makeMassSpectrumSPtr());
  qualified_mass_spectrum.setMsLevel(2);
 
  if(m_cborScanPrecursor.keys().contains("z"))
    {
      precursor_ion_data.charge = m_cborScanPrecursor.value("z").toInteger();
    }
  if(m_cborScanPrecursor.keys().contains("mz"))
    {
      precursor_ion_data.mz = m_cborScanPrecursor.value("mz").toDouble();
    }
  if(m_cborScanPrecursor.keys().contains("intensity"))
    {
      precursor_ion_data.intensity = m_cborScanPrecursor.value("intensity").toDouble();
    }
  qualified_mass_spectrum.appendPrecursorIonData(precursor_ion_data);
  if(m_cborScanMs2.keys().contains("rt"))
    {
      qualified_mass_spectrum.setRtInSeconds(m_cborScanMs2.value("rt").toDouble());
    }
 
 
  return qualified_mass_spectrum.makeQualifiedMassSpectrumSPtr();
}

References pappso::QualifiedMassSpectrum::appendPrecursorIonData(), pappso::PrecursorIonData::charge, pappso::PrecursorIonData::intensity, m_cborScanId, m_cborScanMs2, m_cborScanPrecursor, m_currentPeaklistFile, m_currentSampleName, pappso::MassSpectrum::makeMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::makeQualifiedMassSpectrumSPtr(), pappso::PrecursorIonData::mz, pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MsRunId::setSampleName(), and pappso::MassSpectrumId::setSpectrumIndex().

◆ getPrecursorMass()

double pappso::cbor::psm::PsmFileReaderBase::getPrecursorMass	(	double	mz_prec,
		uint	charge ) const

protected

convenient function do compute precusor ion mass

Definition at line 843 of file psmfilereaderbase.cpp.

{
  // compute precursor mass given the charge state
  mz_prec = mz_prec * (double)charge;
  mz_prec -= (MHPLUS * (double)charge);
  return mz_prec;
}

References pappso::MHPLUS().

◆ informationsReady()

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

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmCbor2Json, pappso::cbor::psm::PsmFileAppend, and pappso::cbor::psm::PsmFileScanProcessAndCopy.

Definition at line 684 of file psmfilereaderbase.cpp.

685{

686}

Referenced by readInformations().

◆ logReady()

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

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmCbor2Json, and pappso::cbor::psm::PsmFileScanProcessAndCopy.

Definition at line 694 of file psmfilereaderbase.cpp.

695{

696}

Referenced by readRoot().

◆ parameterMapReady()

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

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmCbor2Json, pappso::cbor::psm::PsmFeatures, pappso::cbor::psm::PsmFileAppend, pappso::cbor::psm::PsmFileScanProcessAndCopy, pappso::cbor::psm::PsmIonSeries, pappso::cbor::psm::PsmNewEval, pappso::cbor::psm::PsmSpecGlob, and pappso::cbor::psm::PsmSpecPeptidOms.

Definition at line 689 of file psmfilereaderbase.cpp.

690{

691}

Referenced by readParameterMap().

◆ proteinMapReady()

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

protectedvirtual

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

Definition at line 705 of file psmfilereaderbase.cpp.

706{

707}

Referenced by readProteinMap().

◆ psmReady()

void pappso::cbor::psm::PsmFileReaderBase::psmReady ( pappso::UiMonitorInterface & monitor )

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmCbor2Json.

Definition at line 678 of file psmfilereaderbase.cpp.

{
  // PSM is ready, do what you want :)
}

Referenced by readPsm().

◆ readCbor() [1/2]

void pappso::cbor::psm::PsmFileReaderBase::readCbor	(	QFile *	cborp,
		pappso::UiMonitorInterface &	monitor )

Definition at line 70 of file psmfilereaderbase.cpp.

{
  qDebug();
  initCborReader(cborp);
 
  qDebug();
  if(mpa_cborReader->isMap())
    {
      readRoot(monitor);
    }
  qDebug();
}

References pappso::cbor::CborStreamReaderInterface::initCborReader(), pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and readRoot().

◆ readCbor() [2/2]

void pappso::cbor::psm::PsmFileReaderBase::readCbor	(	QIODevice *	cborp,
		pappso::UiMonitorInterface &	monitor )

Definition at line 55 of file psmfilereaderbase.cpp.

{
 
  qDebug();
  initCborReader(cborp);
 
  qDebug();
  if(mpa_cborReader->isMap())
    {
      readRoot(monitor);
    }
  qDebug();
}

References pappso::cbor::CborStreamReaderInterface::initCborReader(), pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and readRoot().

◆ readInformations()

void pappso::cbor::psm::PsmFileReaderBase::readInformations ( pappso::UiMonitorInterface & monitor )

protectedvirtual

Definition at line 194 of file psmfilereaderbase.cpp.

{
  bool is_ok;
  // m_cborInformations.clear();
  is_ok = mpa_cborReader->readCborMap(m_cborInformations);
 
  if(!is_ok)
    {
      throw pappso::PappsoException("ERROR: PSM cbor header informations not well formed");
    }
  qDebug() << m_cborInformations.keys();
  if(m_cborInformations.value("type").toString() != "psm")
    {
      QStringList all_keys;
      for(auto it_k : m_cborInformations.keys())
        {
          all_keys << it_k.toString();
        }
      throw pappso::PappsoException(
        QObject::tr("ERROR: this file does not contain PSM data but %1 and %2")
          .arg(m_cborInformations.value("type").toString())
          .arg(all_keys.join(" ")));
    }
  informationsReady(monitor);
}

References informationsReady(), m_cborInformations, and pappso::cbor::CborStreamReaderInterface::mpa_cborReader.

Referenced by readRoot().

◆ readLog()

void pappso::cbor::psm::PsmFileReaderBase::readLog ( pappso::UiMonitorInterface & monitor )

protectedvirtual

Definition at line 221 of file psmfilereaderbase.cpp.

{
  bool is_ok;
  // m_cborInformations.clear();
  is_ok = mpa_cborReader->readCborArray(m_cborLog);
 
  if(!is_ok)
    {
      throw pappso::PappsoException("ERROR: PSM cbor header log not well formed");
    }
}

References m_cborLog, and pappso::cbor::CborStreamReaderInterface::mpa_cborReader.

Referenced by readRoot().

◆ readParameterMap()

void pappso::cbor::psm::PsmFileReaderBase::readParameterMap ( pappso::UiMonitorInterface & monitor )

protectedvirtual

Definition at line 235 of file psmfilereaderbase.cpp.

{
  bool is_ok;
  m_cborParameterMap.clear();
  is_ok = mpa_cborReader->readCborMap(m_cborParameterMap);
 
  if(!is_ok)
    {
      throw pappso::PappsoException("ERROR: PSM cbor parameter_map not well formed");
    }
  parameterMapReady(monitor);
}

References m_cborParameterMap, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and parameterMapReady().

Referenced by readRoot().

◆ readProteinMap()

void pappso::cbor::psm::PsmFileReaderBase::readProteinMap ( pappso::UiMonitorInterface & monitor )

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmCbor2Json.

Definition at line 249 of file psmfilereaderbase.cpp.

{
  m_proteinMap.readMap(*mpa_cborReader);
  proteinMapReady(monitor);
}

References m_proteinMap, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and proteinMapReady().

Referenced by readRoot().

◆ readPsm()

void pappso::cbor::psm::PsmFileReaderBase::readPsm ( pappso::UiMonitorInterface & monitor )

protectedvirtual

Definition at line 573 of file psmfilereaderbase.cpp.

{
  qDebug();
  bool is_ok;
  if(!mpa_cborReader->isMap())
    {
      throw pappso::PappsoException("ERROR in psm: expecting a map");
    }
  mpa_cborReader->enterContainer();
  getExpectedString();
  //  "proforma": "AQEEM[+15.99491]AQVAK",
  if(m_expectedString == "proforma")
    {
      if(!mpa_cborReader->decodeString(m_currentPsmProforma))
        {
          throw pappso::PappsoException("ERROR: proforma element in psm-scan is not a string");
        }
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting proforma element in psm-scan");
    }
  //"protein_list" : [
  //{
  //"accession": "GRMZM2G083841_P01",
  //"position": [15,236]
  //}
  //],
 
  getExpectedString();
  m_currentPsmProteinRefList.clear();
  qDebug() << m_expectedString;
 
  if(m_expectedString == "protein_list")
    {
      mpa_cborReader->enterContainer(); // array
      while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
        {
          m_currentPsmProteinRefList.push_back(readPsmProteinRef(is_ok));
          if(!is_ok)
            {
              qDebug();
              throw pappso::PappsoException(
                QObject::tr("ERROR: reading protein_list element in psm-scan"));
            }
        }
      // qDebug() << mpa_cborReader->type();
      mpa_cborReader->leaveContainer(); // array
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting protein_list element in psm-scan");
    }
  // props: {
  m_cborScanPsmProps.clear();
 
  //"eval": {
  qDebug();
  m_cborScanPsmEval.clear();
  getExpectedString();
  qDebug() << m_expectedString;
 
  if(m_expectedString == "props")
    {
      is_ok = mpa_cborReader->readCborMap(m_cborScanPsmProps);
      if(!is_ok)
        {
          throw pappso::PappsoException("ERROR: props element in psm-scan is not well formed");
        }
      if(!getExpectedString())
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR: expecting eval element in psm-scan %1").arg(m_currentPsmProforma));
        }
    }
  if(m_expectedString == "eval")
    {
      is_ok = mpa_cborReader->readCborMap(m_cborScanPsmEval);
      if(!is_ok)
        {
          throw pappso::PappsoException("ERROR: eval element in psm-scan is not well formed");
        }
    }
  else
 
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR: expecting eval element in psm-scan %1 not %2 in %3 %4 %5")
          .arg(m_currentPsmProforma)
          .arg(m_expectedString)
          .arg(__FILE__)
          .arg(__FUNCTION__)
          .arg(__LINE__));
    }
 
 
  qDebug() << m_expectedString;
 
 
  mpa_cborReader->leaveContainer();
  qDebug();
  psmReady(monitor);
}

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), m_cborScanPsmEval, m_cborScanPsmProps, m_currentPsmProforma, m_currentPsmProteinRefList, pappso::cbor::CborStreamReaderInterface::m_expectedString, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, psmReady(), and readPsmProteinRef().

Referenced by readScan().

◆ readPsmFile()

PsmFile pappso::cbor::psm::PsmFileReaderBase::readPsmFile ( bool & is_ok )

protected

Definition at line 300 of file psmfilereaderbase.cpp.

{
  is_ok = false;
  PsmFile file;
  mpa_cborReader->enterContainer();
  getExpectedString();
  if(m_expectedString == "name")
    {
      if(!mpa_cborReader->decodeString(file.name))
        {
          throw pappso::PappsoException("file name is not a string");
        }
      is_ok = true;
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting name element in file");
    }
  mpa_cborReader->leaveContainer();
  return file;
}

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::CborStreamReaderInterface::m_expectedString, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and pappso::cbor::psm::PsmFile::name.

Referenced by readSample().

◆ readPsmProteinRef()

PsmFileReaderBase::PsmProteinRef pappso::cbor::psm::PsmFileReaderBase::readPsmProteinRef ( bool & is_ok )

protected

Definition at line 257 of file psmfilereaderbase.cpp.

{
  PsmProteinRef protein_ref;
  protein_ref.accession = "";
  protein_ref.positions.clear();
  mpa_cborReader->enterContainer();
  getExpectedString();
  qDebug() << m_expectedString;
  if(m_expectedString == "accession")
    {
      is_ok = mpa_cborReader->decodeString(protein_ref.accession);
      if(!is_ok)
        {
          throw pappso::PappsoException("ERROR: protein accession is not a string");
        }
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting accession element in PSM protein_list");
    }
 
  getExpectedString();
  qDebug() << m_expectedString;
  if(m_expectedString == "positions")
    {
      mpa_cborReader->readArray(protein_ref.positions);
 
      // mpa_cborReader->next();
    }
  else
    {
      throw pappso::PappsoException(
        QString("ERROR: expecting positions element in PSM protein_list not %1")
          .arg(m_expectedString));
    }
  mpa_cborReader->leaveContainer();
 
  qDebug() << "end";
  return protein_ref;
}

References pappso::cbor::psm::PsmFileReaderBase::PsmProteinRef::accession, pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::CborStreamReaderInterface::m_expectedString, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and pappso::cbor::psm::PsmFileReaderBase::PsmProteinRef::positions.

Referenced by readPsm().

◆ readRoot()

void pappso::cbor::psm::PsmFileReaderBase::readRoot ( pappso::UiMonitorInterface & monitor )

protected

Definition at line 108 of file psmfilereaderbase.cpp.

{
  qDebug();
  mpa_cborReader->enterContainer();
 
  getExpectedString();
  if(m_expectedString == "informations")
    {
      qDebug() << m_expectedString;
      readInformations(monitor);
      getExpectedString();
 
      qDebug() << m_expectedString;
      if(m_expectedString == "log")
        {
          qDebug() << m_expectedString;
          readLog(monitor);
          getExpectedString();
        }
 
      logReady(monitor);
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting informations element");
    }
 
  qDebug() << m_expectedString;
 
  if(m_expectedString == "parameter_map")
    {
      qDebug();
      readParameterMap(monitor);
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting parameter_map element");
    }
 
 
  getExpectedString();
  m_targetFastaFiles.clear();
  m_decoyFastaFiles.clear();
  if(m_expectedString == "target_fasta_files")
    {
      mpa_cborReader->readArray(m_targetFastaFiles);
      getExpectedString();
    }
 
  if(m_expectedString == "decoy_fasta_files")
    {
      mpa_cborReader->readArray(m_decoyFastaFiles);
      getExpectedString();
    }
  fastaFilesReady(monitor);
 
  if(m_expectedString == "protein_map")
    {
      readProteinMap(monitor);
      getExpectedString();
    }
 
  if(m_expectedString == "sample_list")
    {
      sampleListStarted(monitor);
      mpa_cborReader->enterContainer(); // array
      while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
        {
          readSample(monitor);
        }
      mpa_cborReader->leaveContainer(); // array
      sampleListFinished(monitor);
    }
  else
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR: expecting sample_list element not %1").arg(m_expectedString));
    }
  mpa_cborReader->leaveContainer(); // whole file
  if(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
    {
      readRoot(monitor);
    }
}

References fastaFilesReady(), pappso::cbor::CborStreamReaderInterface::getExpectedString(), logReady(), m_decoyFastaFiles, pappso::cbor::CborStreamReaderInterface::m_expectedString, m_targetFastaFiles, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, readInformations(), readLog(), readParameterMap(), readProteinMap(), readRoot(), readSample(), sampleListFinished(), and sampleListStarted().

Referenced by readCbor(), readCbor(), and readRoot().

◆ readSample()

void pappso::cbor::psm::PsmFileReaderBase::readSample ( pappso::UiMonitorInterface & monitor )

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmFileAppend.

Definition at line 346 of file psmfilereaderbase.cpp.

{
  //"name": "tandem2017_nopatch_20120906_balliau_extract_1_A01_urnb-1",
  qDebug();
  mpa_cborReader->enterContainer();
  getExpectedString();
 
  qDebug() << m_expectedString;
  if(m_expectedString == "name")
    {
      if(!mpa_cborReader->decodeString(m_currentSampleName))
        {
          throw pappso::PappsoException("sample name is not a string");
        }
    }
  else
    {
      throw pappso::PappsoException("ERROR reading sample : expecting name element in sample");
    }
  //"identification_file_list": [{ "name":
  //"/home/langella/data1/tandem/tandem2017_nopatch_20120906_balliau_extract_1_A01_urnb-1.xml",
  //}],
 
  getExpectedString();
 
  qDebug() << m_expectedString;
  m_currentIdentificationFileList.clear();
  if(m_expectedString == "identification_file_list")
    {
      bool is_ok;
      mpa_cborReader->enterContainer();
 
      while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
        {
          try
            {
              m_currentIdentificationFileList.push_back(readPsmFile(is_ok));
            }
          catch(const pappso::PappsoException &error)
            {
              throw pappso::PappsoException(
                QObject::tr("ERROR reading sample/identification_file_list : %1")
                  .arg(error.qwhat()));
            }
        }
      mpa_cborReader->leaveContainer();
 
      getExpectedString();
    }
  //"peaklist_file": {"name": "tandem2017_nopatch_20120906_balliau_extract_1_A01_urnb-1.mzml"
  //},
 
  if(m_expectedString == "peaklist_file")
    {
      bool is_ok;
      try
        {
          m_currentPeaklistFile = readPsmFile(is_ok);
        }
      catch(const pappso::PappsoException &error)
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR reading sample/peaklist_file : %1").arg(error.qwhat()));
        }
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting peaklist_file element in sample");
    }
  //"scan_list": [
  sampleStarted(monitor);
  getExpectedString();
  if(m_expectedString == "scan_list")
    {
      if(!mpa_cborReader->isArray())
        {
          throw pappso::PappsoException("ERROR in scan_list: expecting an array");
        }
      mpa_cborReader->enterContainer(); // array
 
      while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
        {
          readScan(monitor);
        }
      mpa_cborReader->leaveContainer();
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting scan_list element in sample");
    }
  mpa_cborReader->leaveContainer();
 
  sampleFinished(monitor);
}

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), m_currentIdentificationFileList, m_currentPeaklistFile, m_currentSampleName, pappso::cbor::CborStreamReaderInterface::m_expectedString, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, pappso::PappsoException::qwhat(), readPsmFile(), readScan(), sampleFinished(), and sampleStarted().

Referenced by readRoot().

◆ readScan()

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

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmFileScanProcess.

Definition at line 442 of file psmfilereaderbase.cpp.

{
  qDebug();
  m_cborScanId.clear();
 
  if(!mpa_cborReader->isMap())
    {
      throw pappso::PappsoException("ERROR in scan: expecting a map");
    }
  mpa_cborReader->enterContainer();
  //"id": {
  //"index": 1976
  //},
  qDebug() << "scan begin";
  QString last_expected_string = m_expectedString;
 
  getExpectedString();
  qDebug() << m_expectedString;
  if(m_expectedString == "id")
    {
      if(!mpa_cborReader->readCborMap(m_cborScanId))
        {
          throw pappso::PappsoException(QObject::tr("id element in scan is not a cbor map"));
        }
    }
  else
    {
      throw pappso::PappsoException(
        QObject::tr(
          "ERROR: expecting id element in scan not %1, sample %2, last expected string %3")
          .arg(m_expectedString)
          .arg(m_currentSampleName)
          .arg(last_expected_string));
    }
  //"precursor": {
  //"z": 2,
  //"mz": 1120.529471
  //},
 
  getExpectedString();
  m_cborScanPrecursor.clear();
  qDebug() << m_expectedString;
  if(m_expectedString == "precursor")
    {
      if(!mpa_cborReader->readCborMap(m_cborScanPrecursor))
        {
          throw pappso::PappsoException(QObject::tr("precursor element in scan is not a cbor map"));
        }
    }
  else
    {
      throw pappso::PappsoException(QObject::tr("ERROR: expecting precursor element after id in "
                                                "scan not %1, sample %2, last expected string %3")
                                      .arg(m_expectedString)
                                      .arg(m_currentSampleName)
                                      .arg(last_expected_string));
    }
  //"ms2": {PSM CBOR format documentation
  //"rt": 12648.87,
  //"mz" :[1,2,3,4],
  //"intensity" : [1,2,3,4]
  //},
 
  getExpectedString();
  qDebug() << m_expectedString;
  m_cborScanMs2.clear();
  if(m_expectedString == "ms2")
    {
      if(!mpa_cborReader->readCborMap(m_cborScanMs2))
        {
          throw pappso::PappsoException(
            QObject::tr("ms2 element after precursor in scan is not a cbor map %1 %2:\n%3")
              .arg(m_currentSampleName)
              .arg(m_cborScanId.value("index").toInteger())
              .arg(mpa_cborReader->lastError().toString()));
        }
    }
  else
    {
      throw pappso::PappsoException(
        QObject::tr(
          "ERROR: expecting ms2 element in scan not %1, sample %2, last expected string %3")
          .arg(m_expectedString)
          .arg(m_currentSampleName)
          .arg(last_expected_string));
    }
 
 
  getExpectedString();
  qDebug() << m_expectedString;
 
 
  if(m_expectedString == "props")
    {
      bool is_ok;
      is_ok = mpa_cborReader->readCborMap(m_cborScanProps);
      if(!is_ok)
        {
          throw pappso::PappsoException("ERROR: props element in scan is not well formed");
        }
      if(!getExpectedString())
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR: expecting psm_list element in scan %1").arg(m_currentPsmProforma));
        }
    }
 
  //"psm_list": [
  scanStarted(monitor);
  if(m_expectedString == "psm_list")
    {
      qDebug() << "psm_list";
      if(!mpa_cborReader->isArray())
        {
          throw pappso::PappsoException("ERROR in psm_list: expecting an array");
        }
      mpa_cborReader->enterContainer();
      while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
        {
          readPsm(monitor);
        }
      mpa_cborReader->leaveContainer();
    }
 
  mpa_cborReader->leaveContainer();
  qDebug() << "scan end";
  scanFinished(monitor);
  qDebug();
}

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), m_cborScanId, m_cborScanMs2, m_cborScanPrecursor, m_cborScanProps, m_currentPsmProforma, m_currentSampleName, pappso::cbor::CborStreamReaderInterface::m_expectedString, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, readPsm(), scanFinished(), and scanStarted().

Referenced by readSample().

◆ sampleFinished()

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

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmCbor2Json, pappso::cbor::psm::PsmFileScanProcess, and pappso::cbor::psm::PsmFileScanProcessAndCopy.

Definition at line 725 of file psmfilereaderbase.cpp.

726{

727}

Referenced by readSample().

◆ sampleListFinished()

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

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmCbor2Json, and pappso::cbor::psm::PsmFileScanProcessAndCopy.

Definition at line 837 of file psmfilereaderbase.cpp.

838{

839}

Referenced by readRoot().

◆ sampleListStarted()

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

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmCbor2Json, and pappso::cbor::psm::PsmFileScanProcessAndCopy.

Definition at line 832 of file psmfilereaderbase.cpp.

833{

834}

Referenced by readRoot().

◆ sampleStarted()

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

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmCbor2Json, and pappso::cbor::psm::PsmFileScanProcessAndCopy.

Definition at line 710 of file psmfilereaderbase.cpp.

711{

712}

Referenced by readSample().

◆ scanFinished()

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

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmCbor2Json, and pappso::cbor::psm::PsmFileScanProcess.

Definition at line 720 of file psmfilereaderbase.cpp.

721{

722}

Referenced by readScan().

◆ scanStarted()

void pappso::cbor::psm::PsmFileReaderBase::scanStarted ( pappso::UiMonitorInterface & monitor )

protectedvirtual

Reimplemented in pappso::cbor::psm::PsmCbor2Json.

Definition at line 715 of file psmfilereaderbase.cpp.

716{

717}

Referenced by readScan().

◆ writePsmFile()

void pappso::cbor::psm::PsmFileReaderBase::writePsmFile	(	CborStreamWriter &	writer,
		const PsmFile &	psm_file )

protected

Definition at line 324 of file psmfilereaderbase.cpp.

{
  writer.startMap();
  writer.append("name");
  writer.append(psm_file.name);
  writer.endMap();
}

References pappso::cbor::psm::PsmFile::name.

Referenced by pappso::cbor::psm::PsmFileScanProcessAndCopy::sampleStarted(), and writePsmFileList().

◆ writePsmFileList()

void pappso::cbor::psm::PsmFileReaderBase::writePsmFileList	(	CborStreamWriter &	writer,
		const std::vector< PsmFile > &	file_list )

protected

Definition at line 333 of file psmfilereaderbase.cpp.

{
  writer.startArray();
  for(auto &psm_file : file_list)
    {
      writePsmFile(writer, psm_file);
    }
  writer.endArray();
}

References writePsmFile().

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

Member Data Documentation

◆ m_cborInformations

QCborMap pappso::cbor::psm::PsmFileReaderBase::m_cborInformations

protected

Definition at line 133 of file psmfilereaderbase.h.

Referenced by pappso::cbor::psm::PsmCbor2Json::informationsReady(), pappso::cbor::psm::PsmFileAppend::informationsReady(), pappso::cbor::psm::PsmFileScanProcessAndCopy::logReady(), and readInformations().

◆ m_cborLog

QCborArray pappso::cbor::psm::PsmFileReaderBase::m_cborLog

protected

Definition at line 134 of file psmfilereaderbase.h.

Referenced by pappso::cbor::psm::PsmCbor2Json::logReady(), pappso::cbor::psm::PsmFileScanProcessAndCopy::logReady(), and readLog().

◆ m_cborParameterMap

QCborMap pappso::cbor::psm::PsmFileReaderBase::m_cborParameterMap

protected

Definition at line 135 of file psmfilereaderbase.h.

Referenced by pappso::cbor::psm::PsmFileAppend::mergeParameterMap(), pappso::cbor::psm::PsmCbor2Json::parameterMapReady(), pappso::cbor::psm::PsmFeatures::parameterMapReady(), pappso::cbor::psm::PsmFileScanProcessAndCopy::parameterMapReady(), pappso::cbor::psm::PsmIonSeries::parameterMapReady(), pappso::cbor::psm::PsmNewEval::parameterMapReady(), pappso::cbor::psm::PsmSpecGlob::parameterMapReady(), pappso::cbor::psm::PsmSpecPeptidOms::parameterMapReady(), and readParameterMap().

◆ m_cborScanId

QCborMap pappso::cbor::psm::PsmFileReaderBase::m_cborScanId

protected

Definition at line 136 of file psmfilereaderbase.h.

Referenced by getCurrentQualifiedMassSpectrumSPtr(), readScan(), and pappso::cbor::psm::PsmCbor2Json::scanStarted().

◆ m_cborScanMs2

QCborMap pappso::cbor::psm::PsmFileReaderBase::m_cborScanMs2

protected

Definition at line 138 of file psmfilereaderbase.h.

Referenced by getCurrentQualifiedMassSpectrumSPtr(), readScan(), and pappso::cbor::psm::PsmCbor2Json::scanStarted().

◆ m_cborScanPrecursor

QCborMap pappso::cbor::psm::PsmFileReaderBase::m_cborScanPrecursor

protected

Definition at line 137 of file psmfilereaderbase.h.

Referenced by getCurrentQualifiedMassSpectrumSPtr(), readScan(), and pappso::cbor::psm::PsmCbor2Json::scanStarted().

◆ m_cborScanProps

QCborMap pappso::cbor::psm::PsmFileReaderBase::m_cborScanProps

protected

Definition at line 139 of file psmfilereaderbase.h.

Referenced by readScan(), and pappso::cbor::psm::PsmCbor2Json::scanStarted().

◆ m_cborScanPsmEval

QCborMap pappso::cbor::psm::PsmFileReaderBase::m_cborScanPsmEval

protected

Definition at line 140 of file psmfilereaderbase.h.

Referenced by pappso::cbor::psm::PsmCbor2Json::psmReady(), and readPsm().

◆ m_cborScanPsmProps

QCborMap pappso::cbor::psm::PsmFileReaderBase::m_cborScanPsmProps

protected

Definition at line 141 of file psmfilereaderbase.h.

Referenced by pappso::cbor::psm::PsmCbor2Json::psmReady(), and readPsm().

◆ m_currentIdentificationFileList

std::vector<PsmFile> pappso::cbor::psm::PsmFileReaderBase::m_currentIdentificationFileList

protected

Definition at line 132 of file psmfilereaderbase.h.

Referenced by readSample(), pappso::cbor::psm::PsmCbor2Json::sampleStarted(), and pappso::cbor::psm::PsmFileScanProcessAndCopy::sampleStarted().

◆ m_currentPeaklistFile

PsmFile pappso::cbor::psm::PsmFileReaderBase::m_currentPeaklistFile

protected

Definition at line 131 of file psmfilereaderbase.h.

Referenced by getCurrentQualifiedMassSpectrumSPtr(), readSample(), pappso::cbor::psm::PsmCbor2Json::sampleStarted(), and pappso::cbor::psm::PsmFileScanProcessAndCopy::sampleStarted().

◆ m_currentPsmProforma

QString pappso::cbor::psm::PsmFileReaderBase::m_currentPsmProforma

protected

Definition at line 142 of file psmfilereaderbase.h.

Referenced by getCurrentPsmPeptideSp(), pappso::cbor::psm::PsmCbor2Json::psmReady(), readPsm(), and readScan().

◆ m_currentPsmProteinRefList

std::vector<PsmProteinRef> pappso::cbor::psm::PsmFileReaderBase::m_currentPsmProteinRefList

protected

Definition at line 143 of file psmfilereaderbase.h.

Referenced by currentProteinRefListContainsDecoy(), currentProteinRefListContainsTarget(), pappso::cbor::psm::PsmCbor2Json::psmReady(), and readPsm().

◆ m_currentSampleName

QString pappso::cbor::psm::PsmFileReaderBase::m_currentSampleName

protected

Definition at line 130 of file psmfilereaderbase.h.

Referenced by getCurrentQualifiedMassSpectrumSPtr(), readSample(), readScan(), pappso::cbor::psm::PsmCbor2Json::sampleStarted(), and pappso::cbor::psm::PsmFileScanProcessAndCopy::sampleStarted().

◆ m_decoyFastaFiles

QStringList pappso::cbor::psm::PsmFileReaderBase::m_decoyFastaFiles

protected

Definition at line 128 of file psmfilereaderbase.h.

Referenced by pappso::cbor::psm::PsmCbor2Json::fastaFilesReady(), pappso::cbor::psm::PsmFileAppend::fastaFilesReady(), pappso::cbor::psm::PsmFileScanProcessAndCopy::fastaFilesReady(), and readRoot().

◆ m_proteinMap

PsmProteinMap pappso::cbor::psm::PsmFileReaderBase::m_proteinMap

protected

Definition at line 129 of file psmfilereaderbase.h.

Referenced by pappso::cbor::psm::PsmFileAppend::close(), currentProteinRefListContainsDecoy(), currentProteinRefListContainsTarget(), pappso::cbor::psm::PsmFileScanProcessAndCopy::processBufferScanDone(), pappso::cbor::psm::PsmFileScanProcessAndCopy::proteinMapReady(), pappso::cbor::psm::PsmSpecPeptidOms::proteinMapReady(), and readProteinMap().

◆ m_targetFastaFiles

QStringList pappso::cbor::psm::PsmFileReaderBase::m_targetFastaFiles

protected

Definition at line 127 of file psmfilereaderbase.h.

Referenced by pappso::cbor::psm::PsmCbor2Json::fastaFilesReady(), pappso::cbor::psm::PsmFileAppend::fastaFilesReady(), pappso::cbor::psm::PsmFileScanProcessAndCopy::fastaFilesReady(), and readRoot().

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

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

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PsmFileReaderBase()

◆ ~PsmFileReaderBase()

Member Function Documentation

◆ currentProteinRefListContainsDecoy()

◆ currentProteinRefListContainsTarget()

◆ fastaFilesReady()

◆ getCurrentPsmPeptideSp()

◆ getCurrentQualifiedMassSpectrumSPtr()

◆ getPrecursorMass()

◆ informationsReady()

◆ logReady()

◆ parameterMapReady()

◆ proteinMapReady()

◆ psmReady()

◆ readCbor() [1/2]

◆ readCbor() [2/2]

◆ readInformations()

◆ readLog()

◆ readParameterMap()

◆ readProteinMap()

◆ readPsm()

◆ readPsmFile()

◆ readPsmProteinRef()

◆ readRoot()

◆ readSample()

◆ readScan()

◆ sampleFinished()

◆ sampleListFinished()

◆ sampleListStarted()

◆ sampleStarted()

◆ scanFinished()

◆ scanStarted()

◆ writePsmFile()

◆ writePsmFileList()

Member Data Documentation

◆ m_cborInformations

◆ m_cborLog

◆ m_cborParameterMap

◆ m_cborScanId

◆ m_cborScanMs2

◆ m_cborScanPrecursor

◆ m_cborScanProps

◆ m_cborScanPsmEval

◆ m_cborScanPsmProps

◆ m_currentIdentificationFileList

◆ m_currentPeaklistFile

◆ m_currentPsmProforma

◆ m_currentPsmProteinRefList

◆ m_currentSampleName

◆ m_decoyFastaFiles

◆ m_proteinMap

◆ m_targetFastaFiles