pappso::cbor::psm::PsmCbor2Json Class Reference

#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
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 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.

{
}

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 pappso::cbor::JsonStreamWriter::endMap().

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);
    }
}

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);
}

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);
}

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);
}

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();
}

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")
    {
      QCborArray cbor_protein_list;
      mpa_cborReader->readCborArray(cbor_protein_list);
      mp_jsonOutput->writeCborArray(cbor_protein_list);
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting protein_list element in psm-scan");
    }
  //"eval": {
  qDebug();
  m_cborScanPsmProps.clear();
  m_cborScanPsmEval.clear();
  if(!getExpectedString())
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR: expecting props or eval element in psm-scan %1")
          .arg(m_currentPsmProforma));
    }
  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");
        }
      mp_jsonOutput->appendKey(m_expectedString);
      mp_jsonOutput->writeCborMap(m_cborScanPsmProps);
      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);
}

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);
}

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();
}

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();
}

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();
}

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().

---

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