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
	convenient function to clean pointer before leaving
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	informationsReady (pappso::UiMonitorInterface &monitor) override
void	logReady (pappso::UiMonitorInterface &monitor) override
void	parameterMapReady (pappso::UiMonitorInterface &monitor) override
void	fastaFilesReady (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
void	scanStarted (pappso::UiMonitorInterface &monitor) override
void	scanFinished (pappso::UiMonitorInterface &monitor) override
void	psmReady (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	readSample (pappso::UiMonitorInterface &monitor)
virtual void	readScan (pappso::UiMonitorInterface &monitor)
virtual void	readPsm (pappso::UiMonitorInterface &monitor)
virtual void	proteinMapReady (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
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_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 41 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

convenient function to clean pointer before leaving

Reimplemented from pappso::cbor::CborStreamReaderInterface.

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 71 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 80 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 88 of file psmcbor2json.cpp.

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

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

psmReady()

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

overrideprotectedvirtual

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

Definition at line 206 of file psmcbor2json.cpp.

{
  mp_jsonOutput->startMap(); // psm
  mp_jsonOutput->appendKey("proforma");
  mp_jsonOutput->appendValue(m_currentPsmProforma);
  mp_jsonOutput->appendKey("protein_list");
  mp_jsonOutput->startArray();
  for(auto &protein_ref : m_currentPsmProteinRefList)
    {
      mp_jsonOutput->startMap();
      mp_jsonOutput->appendKey("accession");
      mp_jsonOutput->appendValue(protein_ref.accession);
      mp_jsonOutput->appendKey("positions");
      mp_jsonOutput->startArray();
      for(auto position : protein_ref.positions)
        {
          mp_jsonOutput->appendValue(position);
        }
      mp_jsonOutput->endArray();
      mp_jsonOutput->endMap();
    }
  mp_jsonOutput->endArray();
  if(!m_cborScanPsmProps.isEmpty())
    {
      mp_jsonOutput->appendKey("props");
      mp_jsonOutput->writeCborMap(m_cborScanPsmProps);
    }
  mp_jsonOutput->appendKey("eval");
  mp_jsonOutput->writeCborMap(m_cborScanPsmEval);
 
  mp_jsonOutput->endMap(); // psm
}

References pappso::cbor::psm::PsmFileReaderBase::m_cborScanPsmEval, pappso::cbor::psm::PsmFileReaderBase::m_cborScanPsmProps, pappso::cbor::psm::PsmFileReaderBase::m_currentPsmProforma, pappso::cbor::psm::PsmFileReaderBase::m_currentPsmProteinRefList, and mp_jsonOutput.

readProteinMap()

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

overrideprotectedvirtual

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

Definition at line 113 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.

sampleFinished()

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

overrideprotectedvirtual

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

Definition at line 198 of file psmcbor2json.cpp.

{
  mp_jsonOutput->endArray(); // scan_list
  mp_jsonOutput->endMap();   // sample
}

References mp_jsonOutput.

sampleListFinished()

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

overrideprotectedvirtual

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

Definition at line 105 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 96 of file psmcbor2json.cpp.

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

References mp_jsonOutput.

sampleStarted()

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

overrideprotectedvirtual

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

Definition at line 166 of file psmcbor2json.cpp.

{
  //"name": "tandem2017_nopatch_20120906_balliau_extract_1_A01_urnb-1",
  qDebug();
  mp_jsonOutput->startMap(); // sample
  mp_jsonOutput->appendKey("name");
  mp_jsonOutput->appendValue(m_currentSampleName);
 
 
  mp_jsonOutput->appendKey("identification_file_list");
  mp_jsonOutput->startArray();
  for(auto &identification_file : m_currentIdentificationFileList)
    {
      mp_jsonOutput->startMap();
      mp_jsonOutput->appendKey("name");
      mp_jsonOutput->appendValue(identification_file.name);
      mp_jsonOutput->endMap();
    }
  mp_jsonOutput->endArray();
 
 
  mp_jsonOutput->appendKey("peaklist_file");
  mp_jsonOutput->startMap();
  mp_jsonOutput->appendKey("name");
  mp_jsonOutput->appendValue(m_currentPeaklistFile.name);
  mp_jsonOutput->endMap();
 
  mp_jsonOutput->appendKey("scan_list");
  mp_jsonOutput->startArray();
}

References pappso::cbor::psm::PsmFileReaderBase::m_currentIdentificationFileList, pappso::cbor::psm::PsmFileReaderBase::m_currentPeaklistFile, pappso::cbor::psm::PsmFileReaderBase::m_currentSampleName, and mp_jsonOutput.

scanFinished()

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

overrideprotectedvirtual

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

Definition at line 158 of file psmcbor2json.cpp.

{
  mp_jsonOutput->endArray(); // psm_list
  mp_jsonOutput->endMap();   // scan
}

References mp_jsonOutput.

scanStarted()

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

overrideprotectedvirtual

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

Definition at line 138 of file psmcbor2json.cpp.

{
 
  mp_jsonOutput->startMap();
  mp_jsonOutput->appendKey("id");
  mp_jsonOutput->writeCborMap(m_cborScanId);
  mp_jsonOutput->appendKey("precursor");
  mp_jsonOutput->writeCborMap(m_cborScanPrecursor);
  mp_jsonOutput->appendKey("ms2");
  mp_jsonOutput->writeCborMap(m_cborScanMs2);
  if(!m_cborScanProps.isEmpty())
    {
      mp_jsonOutput->appendKey("props");
      mp_jsonOutput->writeCborMap(m_cborScanProps);
    };
  mp_jsonOutput->appendKey("psm_list");
  mp_jsonOutput->startArray();
}

References pappso::cbor::psm::PsmFileReaderBase::m_cborScanId, pappso::cbor::psm::PsmFileReaderBase::m_cborScanMs2, pappso::cbor::psm::PsmFileReaderBase::m_cborScanPrecursor, pappso::cbor::psm::PsmFileReaderBase::m_cborScanProps, and mp_jsonOutput.

Member Data Documentation

mp_jsonOutput

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

protected

Definition at line 78 of file psmcbor2json.h.

Referenced by PsmCbor2Json(), close(), fastaFilesReady(), informationsReady(), logReady(), parameterMapReady(), psmReady(), readProteinMap(), sampleFinished(), sampleListFinished(), sampleListStarted(), sampleStarted(), scanFinished(), and scanStarted().

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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