#include <psmcbor2json.h>

Inheritance diagram for pappso::cbor::psm::PsmCbor2Json:

Public Member Functions
	PsmCbor2Json (pappso::cbor::JsonStreamWriter *json_output_p)

virtual	~PsmCbor2Json ()

void	close () override

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	readSample (pappso::UiMonitorInterface &monitor) override

void	sampleListStarted (pappso::UiMonitorInterface &monitor) override

void	sampleListFinished (pappso::UiMonitorInterface &monitor) override

void	readScan (pappso::UiMonitorInterface &monitor) override

void	readPsm (pappso::UiMonitorInterface &monitor) override

void	readProteinMap (pappso::UiMonitorInterface &monitor) override

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	psmReady (pappso::UiMonitorInterface &monitor)

virtual void	proteinMapReady (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)

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
pappso::cbor::JsonStreamWriter *	mp_jsonOutput

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

Todo: write docs

Definition at line 40 of file psmcbor2json.h.

Constructor & Destructor Documentation

◆ PsmCbor2Json()

pappso::cbor::psm::PsmCbor2Json::PsmCbor2Json ( pappso::cbor::JsonStreamWriter * json_output_p )

Default constructor

Definition at line 35 of file psmcbor2json.cpp.

{
  mp_jsonOutput = json_output_p;
 
  *mp_jsonOutput << "{" << Qt::endl;
}

References mp_jsonOutput.

◆ ~PsmCbor2Json()

pappso::cbor::psm::PsmCbor2Json::~PsmCbor2Json ( )

virtual

Destructor

Definition at line 43 of file psmcbor2json.cpp.

44{

45}

Member Function Documentation

◆ close()

void pappso::cbor::psm::PsmCbor2Json::close ( )

overridevirtual

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

Definition at line 48 of file psmcbor2json.cpp.

{
 
  mp_jsonOutput->endMap();
}

References mp_jsonOutput.

◆ fastaFilesReady()

void pappso::cbor::psm::PsmCbor2Json::fastaFilesReady ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 55 of file psmcbor2json.cpp.

{
  if(!m_targetFastaFiles.isEmpty())
    {
      mp_jsonOutput->appendKey("target_fasta_files");
      mp_jsonOutput->writeArray(m_targetFastaFiles);
    }
  if(!m_decoyFastaFiles.isEmpty())
    {
      mp_jsonOutput->appendKey("decoy_fasta_files");
      mp_jsonOutput->writeArray(m_decoyFastaFiles);
    }
}

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

◆ informationsReady()

void pappso::cbor::psm::PsmCbor2Json::informationsReady ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 70 of file psmcbor2json.cpp.

{
 
  mp_jsonOutput->appendKey("informations");
  mp_jsonOutput->writeCborMap(m_cborInformations);
}

References pappso::cbor::psm::PsmFileReaderBase::m_cborInformations, and mp_jsonOutput.

◆ logReady()

void pappso::cbor::psm::PsmCbor2Json::logReady ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 78 of file psmcbor2json.cpp.

{
  mp_jsonOutput->appendKey("log");
  mp_jsonOutput->writeCborArray(m_cborLog);
}

References pappso::cbor::psm::PsmFileReaderBase::m_cborLog, and mp_jsonOutput.

◆ parameterMapReady()

void pappso::cbor::psm::PsmCbor2Json::parameterMapReady ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 86 of file psmcbor2json.cpp.

{
  mp_jsonOutput->appendKey("parameter_map");
  mp_jsonOutput->writeCborMap(m_cborParameterMap);
}

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

◆ readProteinMap()

void pappso::cbor::psm::PsmCbor2Json::readProteinMap ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 108 of file psmcbor2json.cpp.

{
  mp_jsonOutput->appendKey("protein_map");
  mp_jsonOutput->startMap();
  if(!mpa_cborReader->enterContainer())
    {
      throw pappso::PappsoException(QObject::tr("enterContainer in protein map failed"));
    }
  QString accession;
  while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
    {
      mpa_cborReader->decodeString(accession);
      mp_jsonOutput->appendKey(accession);
 
      QCborMap cbor_protein;
      mpa_cborReader->readCborMap(cbor_protein);
      mp_jsonOutput->writeCborMap(cbor_protein);
    }
 
  mpa_cborReader->leaveContainer();
  mp_jsonOutput->endMap();
}

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

◆ readPsm()

void pappso::cbor::psm::PsmCbor2Json::readPsm ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 315 of file psmcbor2json.cpp.

{
  bool is_ok;
  mpa_cborReader->enterContainer();
  mp_jsonOutput->startMap();
  getExpectedString();
  mp_jsonOutput->appendKey(m_expectedString);
  //  "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");
        }
      mp_jsonOutput->appendValue(m_currentPsmProforma);
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting proforma element in psm-scan");
    }
  //"protein_list" : [
  //{
  //"accession": "GRMZM2G083841_P01",
  //"position": [15,236]
  //}
  //],
 
  getExpectedString();
  mp_jsonOutput->appendKey(m_expectedString);
  m_currentPsmProteinRefList.clear();
  qDebug() << m_expectedString;
  if(m_expectedString == "protein_list")
    {
      mpa_cborReader->enterContainer();
      mp_jsonOutput->startArray();
      QCborMap cbor_protein;
      while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
        {
          mpa_cborReader->readCborMap(cbor_protein);
          mp_jsonOutput->writeCborMap(cbor_protein);
        }
      mpa_cborReader->leaveContainer();
      mp_jsonOutput->endArray();
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting protein_list element in psm-scan");
    }
  //"eval": {
  qDebug();
  m_cborScanPsmEval.clear();
  if(!getExpectedString())
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR: expecting eval element in psm-scan %1").arg(m_currentPsmProforma));
    }
  mp_jsonOutput->appendKey(m_expectedString);
  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");
        }
      mp_jsonOutput->writeCborMap(m_cborScanPsmEval);
    }
 
  qDebug() << m_expectedString;
 
 
  mpa_cborReader->leaveContainer();
  mp_jsonOutput->endMap();
  qDebug();
  psmReady(monitor);
}

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::psm::PsmFileReaderBase::m_cborScanPsmEval, pappso::cbor::psm::PsmFileReaderBase::m_currentPsmProforma, pappso::cbor::psm::PsmFileReaderBase::m_currentPsmProteinRefList, pappso::cbor::CborStreamReaderInterface::m_expectedString, mp_jsonOutput, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and pappso::cbor::psm::PsmFileReaderBase::psmReady().

Referenced by readScan().

◆ readSample()

void pappso::cbor::psm::PsmCbor2Json::readSample ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 234 of file psmcbor2json.cpp.

{
  //"name": "tandem2017_nopatch_20120906_balliau_extract_1_A01_urnb-1",
  qDebug();
  mpa_cborReader->enterContainer();
  mp_jsonOutput->startMap();
  getExpectedString();
 
  qDebug() << m_expectedString;
  mp_jsonOutput->appendKey(m_expectedString);
  if(m_expectedString == "name")
    {
      if(!mpa_cborReader->decodeString(m_currentSampleName))
        {
          throw pappso::PappsoException("sample name is not a string");
        }
      mp_jsonOutput->appendValue(m_currentSampleName);
    }
  else
    {
      throw pappso::PappsoException("ERROR: 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())
        {
          m_currentIdentificationFileList.push_back(readPsmFile(is_ok));
        }
      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;
      m_currentPeaklistFile = readPsmFile(is_ok);
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting peaklist_file element in sample");
    }
  //"scan_list": [
  sampleStarted(monitor);
  getExpectedString();
  mp_jsonOutput->appendKey(m_expectedString);
  if(m_expectedString == "scan_list")
    {
      mpa_cborReader->enterContainer();
      mp_jsonOutput->startArray();
      while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
        {
          readScan(monitor);
        }
      mpa_cborReader->leaveContainer();
      mp_jsonOutput->endArray();
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting scan_list element in sample");
    }
  mpa_cborReader->leaveContainer();
  mp_jsonOutput->endMap();
 
  sampleFinished(monitor);
}

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

◆ readScan()

void pappso::cbor::psm::PsmCbor2Json::readScan ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 133 of file psmcbor2json.cpp.

{
  qDebug();
  m_cborScanId.clear();
  if(!mpa_cborReader->enterContainer())
    {
      throw pappso::PappsoException(QObject::tr("enterContainer in scan failed"));
    }
  mp_jsonOutput->startMap();
  //"id": {
  //"index": 1976
  //},
  qDebug() << "scan begin";
 
  if(!getExpectedString())
    {
      throw pappso::PappsoException(QObject::tr("getExpectedString in scan failed"));
    }
  qDebug() << m_expectedString;
 
  mp_jsonOutput->appendKey(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"));
        }
 
      mp_jsonOutput->writeCborMap(m_cborScanId);
    }
  else
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR: expecting id element in scan not %1").arg(m_expectedString));
    }
  //"precursor": {
  //"z": 2,
  //"mz": 1120.529471
  //},
 
  getExpectedString();
  m_cborScanPrecursor.clear();
  qDebug() << m_expectedString;
  mp_jsonOutput->appendKey(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"));
        }
      mp_jsonOutput->writeCborMap(m_cborScanPrecursor);
    }
  //"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();
  mp_jsonOutput->appendKey(m_expectedString);
  if(m_expectedString == "ms2")
    {
      if(!mpa_cborReader->readCborMap(m_cborScanMs2))
        {
          throw pappso::PappsoException(
            QObject::tr("ms2 element 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()));
        }
      mp_jsonOutput->writeCborMap(m_cborScanMs2);
    }
  //"psm_list": [
  scanStarted(monitor);
 
  getExpectedString();
  qDebug() << m_expectedString;
  mp_jsonOutput->appendKey(m_expectedString);
  if(m_expectedString == "psm_list")
    {
      mpa_cborReader->enterContainer();
      mp_jsonOutput->startArray();
      while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
        {
          readPsm(monitor);
        }
      mpa_cborReader->leaveContainer();
      mp_jsonOutput->endArray();
    }
 
  mpa_cborReader->leaveContainer();
  mp_jsonOutput->endMap();
  qDebug() << "scan end";
  scanFinished(monitor);
  qDebug();
}

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

Referenced by readSample().

◆ sampleListFinished()

void pappso::cbor::psm::PsmCbor2Json::sampleListFinished ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 101 of file psmcbor2json.cpp.

{
 
  mp_jsonOutput->endArray();
}

References mp_jsonOutput.

◆ sampleListStarted()

void pappso::cbor::psm::PsmCbor2Json::sampleListStarted ( pappso::UiMonitorInterface & monitor )

overrideprotectedvirtual

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

Definition at line 93 of file psmcbor2json.cpp.

{
 
  mp_jsonOutput->appendKey("sample_list");
  mp_jsonOutput->startArray();
}

References mp_jsonOutput.

Member Data Documentation

◆ mp_jsonOutput

pappso::cbor::JsonStreamWriter* pappso::cbor::psm::PsmCbor2Json::mp_jsonOutput

protected

Definition at line 70 of file psmcbor2json.h.

Referenced by PsmCbor2Json(), close(), fastaFilesReady(), informationsReady(), logReady(), parameterMapReady(), readProteinMap(), readPsm(), readSample(), readScan(), sampleListFinished(), and sampleListStarted().

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

pappsomspp/core/processing/cbor/psm/psmcbor2json.h
pappsomspp/core/processing/cbor/psm/psmcbor2json.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PsmCbor2Json()

◆ ~PsmCbor2Json()

Member Function Documentation

◆ close()

◆ fastaFilesReady()

◆ informationsReady()

◆ logReady()

◆ parameterMapReady()

◆ readProteinMap()

◆ readPsm()

◆ readSample()

◆ readScan()

◆ sampleListFinished()

◆ sampleListStarted()

Member Data Documentation

◆ mp_jsonOutput