#include <psmfileappend.h>

Inheritance diagram for pappso::cbor::psm::PsmFileAppend:

Classes
struct	SampleStorage

Public Member Functions
	PsmFileAppend (pappso::cbor::CborStreamWriter *p_output)

virtual	~PsmFileAppend ()

void	informationsReady (pappso::UiMonitorInterface &monitor) override

void	parameterMapReady (pappso::UiMonitorInterface &monitor) override

void	fastaFilesReady (pappso::UiMonitorInterface &monitor) override

void	readSample (pappso::UiMonitorInterface &monitor) override

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	mergeParameterMap ()

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	readScan (pappso::UiMonitorInterface &monitor)

virtual void	readPsm (pappso::UiMonitorInterface &monitor)

virtual void	psmReady (pappso::UiMonitorInterface &monitor)

virtual void	logReady (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

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)

Private Attributes
QTemporaryDir *	mpa_temporaryDirectory

pappso::cbor::CborStreamWriter *	mp_output

bool	m_isInformations = false

QCborMap	m_outputParameterMap

QStringList	m_outputTargetFastaFiles

QStringList	m_outputDecoyFastaFiles

std::vector< SampleStorage >	m_sampleStorageList

Additional Inherited Members
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 38 of file psmfileappend.h.

Constructor & Destructor Documentation

◆ PsmFileAppend()

pappso::cbor::psm::PsmFileAppend::PsmFileAppend ( pappso::cbor::CborStreamWriter * p_output )

Default constructor

Definition at line 31 of file psmfileappend.cpp.

{
  mp_output = p_output;
 
  mp_output->startMap();
 
  mpa_temporaryDirectory = new QTemporaryDir();
  mpa_temporaryDirectory->setAutoRemove(false);
}

References mp_output, and mpa_temporaryDirectory.

◆ ~PsmFileAppend()

pappso::cbor::psm::PsmFileAppend::~PsmFileAppend ( )

virtual

Destructor

Definition at line 41 of file psmfileappend.cpp.

{
  delete mpa_temporaryDirectory;
}

References mpa_temporaryDirectory.

Member Function Documentation

◆ close()

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

overridevirtual

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

Definition at line 67 of file psmfileappend.cpp.

{
 
 
  qDebug();
  mp_output->append("parameter_map");
  mp_output->writeCborMap(m_outputParameterMap);
 
 
  if(!m_outputTargetFastaFiles.isEmpty())
    {
      mp_output->append("target_fasta_files");
      mp_output->writeArray(m_outputTargetFastaFiles);
    }
  if(!m_outputDecoyFastaFiles.isEmpty())
    {
      mp_output->append("decoy_fasta_files");
      mp_output->writeArray(m_outputDecoyFastaFiles);
    }
 
  mp_output->append("protein_map");
  m_proteinMap.writeMap(*mp_output);
 
  qDebug();
  mp_output->append("sample_list");
  mp_output->startArray();
  for(auto &tmp_sample : m_sampleStorageList)
    {
      QFile store_sample_file(tmp_sample.temporaryFile);
      store_sample_file.open(QIODevice::ReadOnly);
      CborStreamReader tmp_reader(&store_sample_file);
      if(tmp_reader.isTag() && tmp_reader.toTag() == QCborKnownTags::Signature)
        tmp_reader.next();
      QCborMap cbor_sample;
      if(!tmp_reader.readCborMap(cbor_sample))
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR writing sample %1").arg(tmp_sample.fileId));
        }
      mp_output->writeCborMap(cbor_sample);
      store_sample_file.close();
    }
  mp_output->endArray();
 
 
  qDebug();
  mp_output->endMap();
}

References m_outputDecoyFastaFiles, m_outputParameterMap, m_outputTargetFastaFiles, pappso::cbor::psm::PsmFileReaderBase::m_proteinMap, m_sampleStorageList, mp_output, and pappso::cbor::CborStreamReader::readCborMap().

◆ fastaFilesReady()

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

overridevirtual

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

Definition at line 129 of file psmfileappend.cpp.

{
  m_outputDecoyFastaFiles  = m_decoyFastaFiles;
  m_outputTargetFastaFiles = m_targetFastaFiles;
}

References pappso::cbor::psm::PsmFileReaderBase::m_decoyFastaFiles, m_outputDecoyFastaFiles, m_outputTargetFastaFiles, and pappso::cbor::psm::PsmFileReaderBase::m_targetFastaFiles.

◆ informationsReady()

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

overridevirtual

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

Definition at line 47 of file psmfileappend.cpp.

{
  if(!m_isInformations)
    {
      mp_output->append("informations");
      mp_output->writeCborMap(m_cborInformations);
      m_isInformations = true;
    }
}

References pappso::cbor::psm::PsmFileReaderBase::m_cborInformations, m_isInformations, and mp_output.

◆ mergeParameterMap()

void pappso::cbor::psm::PsmFileAppend::mergeParameterMap ( )

protected

Definition at line 117 of file psmfileappend.cpp.

{
  for(auto cbor_key : m_cborParameterMap.keys())
    {
      if(!m_outputParameterMap.contains(cbor_key))
        {
          m_outputParameterMap.insert(cbor_key, m_cborParameterMap.value(cbor_key));
        }
    }
}

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

Referenced by parameterMapReady().

◆ parameterMapReady()

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

overridevirtual

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

Definition at line 59 of file psmfileappend.cpp.

{
  mergeParameterMap();
}

References mergeParameterMap().

◆ readSample()

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

overridevirtual

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

Definition at line 137 of file psmfileappend.cpp.

{
  QCborMap cbor_current_sample;
 
  mpa_cborReader->readCborMap(cbor_current_sample);
 
  SampleStorage sample_file;
  sample_file.fileId  = cbor_current_sample.value("name").toString();
  QString sample_name = sample_file.fileId;
  auto it             = std::find_if(m_sampleStorageList.begin(),
                         m_sampleStorageList.end(),
                         [sample_name](const SampleStorage &sample) {
                           if(sample.fileId == sample_name)
                             return true;
                           return false;
                         });
  if(it != m_sampleStorageList.end())
    {
      throw pappso::PappsoException(
        QObject::tr("adding the same sample twice is forbidden %1").arg(sample_name));
    }
  sample_file.temporaryFile =
    mpa_temporaryDirectory->filePath(QString("file_%1").arg(m_sampleStorageList.size()));
  m_sampleStorageList.push_back(sample_file);
 
  QFile store_sample_file(sample_file.temporaryFile);
  store_sample_file.open(QIODevice::WriteOnly);
  CborStreamWriter tmp_writer(&store_sample_file);
  tmp_writer.writeCborMap(cbor_current_sample);
  store_sample_file.close();
}

References pappso::cbor::psm::PsmFileAppend::SampleStorage::fileId, m_sampleStorageList, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, mpa_temporaryDirectory, pappso::cbor::psm::PsmFileAppend::SampleStorage::temporaryFile, and pappso::cbor::CborStreamWriter::writeCborMap().

Member Data Documentation

◆ m_isInformations

bool pappso::cbor::psm::PsmFileAppend::m_isInformations = false

private

Definition at line 73 of file psmfileappend.h.

Referenced by informationsReady().

◆ m_outputDecoyFastaFiles

QStringList pappso::cbor::psm::PsmFileAppend::m_outputDecoyFastaFiles

private

Definition at line 77 of file psmfileappend.h.

Referenced by close(), and fastaFilesReady().

◆ m_outputParameterMap

QCborMap pappso::cbor::psm::PsmFileAppend::m_outputParameterMap

private

Definition at line 75 of file psmfileappend.h.

Referenced by close(), and mergeParameterMap().

◆ m_outputTargetFastaFiles

QStringList pappso::cbor::psm::PsmFileAppend::m_outputTargetFastaFiles

private

Definition at line 76 of file psmfileappend.h.

Referenced by close(), and fastaFilesReady().

◆ m_sampleStorageList

std::vector<SampleStorage> pappso::cbor::psm::PsmFileAppend::m_sampleStorageList

private

Definition at line 78 of file psmfileappend.h.

Referenced by close(), and readSample().

◆ mp_output

pappso::cbor::CborStreamWriter* pappso::cbor::psm::PsmFileAppend::mp_output

private

Definition at line 71 of file psmfileappend.h.

Referenced by PsmFileAppend(), close(), and informationsReady().

◆ mpa_temporaryDirectory

QTemporaryDir* pappso::cbor::psm::PsmFileAppend::mpa_temporaryDirectory

private

Definition at line 70 of file psmfileappend.h.

Referenced by PsmFileAppend(), ~PsmFileAppend(), and readSample().

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

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

Classes

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PsmFileAppend()

◆ ~PsmFileAppend()

Member Function Documentation

◆ close()

◆ fastaFilesReady()

◆ informationsReady()

◆ mergeParameterMap()

◆ parameterMapReady()

◆ readSample()

Member Data Documentation

◆ m_isInformations

◆ m_outputDecoyFastaFiles

◆ m_outputParameterMap

◆ m_outputTargetFastaFiles

◆ m_sampleStorageList

◆ mp_output

◆ mpa_temporaryDirectory