pappso::masschroq::CborOutputStream Class Reference

#include <cboroutputstream.h>

Public Member Functions
	CborOutputStream (QIODevice *device)
virtual	~CborOutputStream ()
void	setIsTraceOutput (bool is_trace_output)
	set trace output flag More...
void	setIsPeakShapeOutput (bool is_shape_output, double margin_in_seconds)
	set peak shape output flag More...
void	writeJsonObject (const QString &name, const QJsonObject &json_object)
void	writeProjectParameters (const pappso::ProjectParameters &project_parameters)
void	writeActionBegin (const QString &operation)
void	close ()
QCborStreamWriter &	getCborStreamWriter ()
void	writeQrDataBlock (pappso::UiMonitorInterface &m_uiMonitor, const MsRunPeptideList &msrun_peptide_list, bool is_mbr)
void	writeMsRunRetentionTime (const pappso::Trace &report_common_ms2, const pappso::MsRunRetentionTime< QString > &msrun_retention_time)

Private Member Functions
void	writeMbrPeptideMeasurements (const MbrPeptideMeasurements &peptide_measurements, const pappso::MsRunRetentionTime< QString > *msrun_retention_time_p)
void	writeMeasurement (const PeptideMeasurements::Measurement &measurement, const pappso::MsRunRetentionTime< QString > *msrun_retention_time_p)
void	writeTrace (const pappso::Trace &trace)
void	writeVectorDouble (const std::vector< double > &vector)
void	writeTracePeak (const pappso::TracePeak &peak, const pappso::MsRunRetentionTime< QString > *msrun_retention_time_p)
void	writeActionEnd ()
void	writeMsRun (const MsRun &msrun)
void	writePeptideMeasurements (const PeptideMeasurements &peptide_measurements, const pappso::MsRunRetentionTime< QString > *msrun_retention_time_p)

Private Attributes
pappso::cbor::CborStreamWriter *	mpa_writer = nullptr
bool	m_isTraceOutput = false
bool	m_isPeakShapeOutput = false
bool	m_isXicCoordOutput = true
double	m_peakShapeMarginInSeconds = 20

Detailed Description

Todo:

write docs

Definition at line 50 of file cboroutputstream.h.

Constructor & Destructor Documentation

CborOutputStream()

pappso::masschroq::CborOutputStream::CborOutputStream

(

QIODevice *

device

)

Default constructor

Definition at line 40 of file cboroutputstream.cpp.

{
  mpa_writer = new pappso::cbor::CborStreamWriter(device);
  mpa_writer->startMap();
}

References mpa_writer.

~CborOutputStream()

pappso::masschroq::CborOutputStream::~CborOutputStream ( )

virtual

Destructor

Definition at line 46 of file cboroutputstream.cpp.

{
}

Member Function Documentation

close()

void pappso::masschroq::CborOutputStream::close

(

)

Definition at line 82 of file cboroutputstream.cpp.

{
  writeActionEnd();
  mpa_writer->endMap();
 
  delete mpa_writer;
}

getCborStreamWriter()

QCborStreamWriter & pappso::masschroq::CborOutputStream::getCborStreamWriter

(

)

Definition at line 101 of file cboroutputstream.cpp.

{
  return (*mpa_writer);
}

Referenced by pappso::masschroq::JsonInput::action(), pappso::masschroq::MsRunGroup::align(), pappso::masschroq::MsRunGroup::alignRetentionTimeBetweenMsRuns(), pappso::masschroq::MsRunGroup::quantify(), and pappso::masschroq::JsonInput::readAction().

setIsPeakShapeOutput()

void pappso::masschroq::CborOutputStream::setIsPeakShapeOutput	(	bool	is_shape_output,
		double	margin_in_seconds
	)

set peak shape output flag

Definition at line 51 of file cboroutputstream.cpp.

{
  m_isPeakShapeOutput        = is_shape_output;
  m_peakShapeMarginInSeconds = margin_in_seconds;
}

setIsTraceOutput()

void pappso::masschroq::CborOutputStream::setIsTraceOutput

(

bool

is_trace_output

)

set trace output flag

Definition at line 59 of file cboroutputstream.cpp.

{
  m_isTraceOutput = is_trace_output;
}

writeActionBegin()

void pappso::masschroq::CborOutputStream::writeActionBegin

(

const QString &

operation

)

Definition at line 65 of file cboroutputstream.cpp.

{
  mpa_writer->writeInformations(
    "masschroq", pappso::masschroq::Utils::getVersion(), "quantification", "quantification");
}

References pappso::masschroq::Utils::getVersion().

Referenced by pappso::masschroq::JsonInput::action().

writeActionEnd()

void pappso::masschroq::CborOutputStream::writeActionEnd ( )

private

Definition at line 73 of file cboroutputstream.cpp.

{
  mpa_writer->append(QLatin1String("end"));
  mpa_writer->startMap();
  mpa_writer->append(QLatin1String("timestamp"));
  mpa_writer->append(QDateTime::currentDateTime().toString(Qt::ISODate));
  mpa_writer->endMap();
}

writeJsonObject()

void pappso::masschroq::CborOutputStream::writeJsonObject	(	const QString &	name,
		const QJsonObject &	json_object
	)

Definition at line 91 of file cboroutputstream.cpp.

{
  mpa_writer->append(name);
  QCborMap map;
  map = map.fromJsonObject(json_object);
  map.toCborValue().toCbor(*mpa_writer);
}

Referenced by pappso::masschroq::JsonInput::action().

writeMbrPeptideMeasurements()

void pappso::masschroq::CborOutputStream::writeMbrPeptideMeasurements ( const MbrPeptideMeasurements &  peptide_measurements, const pappso::MsRunRetentionTime< QString > *  msrun_retention_time_p  )

private

Definition at line 300 of file cboroutputstream.cpp.

{
  pappso::masschroq::PeptideSp peptide_sp = mbr_peptide_measurements.getPeptideSp();
 
  mpa_writer->append(peptide_sp.get()->getId());
  mpa_writer->startMap();
  mpa_writer->append(QLatin1String("proforma"));
  mpa_writer->append(peptide_sp.get()->getPappsoPeptideSp().get()->toProForma());
 
 
  mpa_writer->append(QLatin1String("mods"));
  mpa_writer->append(peptide_sp.get()->getMods());
 
 
  std::size_t size_measurement = mbr_peptide_measurements.getMeasurementList().size();
  if(size_measurement > 0)
    {
      mpa_writer->append(QLatin1String("rt_target"));
      mpa_writer->append(
        mbr_peptide_measurements.getMeasurementList().at(0).msp_xicCoord.get()->rtTarget);
    }
 
  mpa_writer->append(QLatin1String("xics"));
  mpa_writer->startArray(mbr_peptide_measurements.getMeasurementList().size());
  for(const pappso::masschroq::PeptideMeasurements::Measurement &measure :
      mbr_peptide_measurements.getMeasurementList())
    {
      // write(peptide_sp, measure, msrun_retention_time_p);
      writeMeasurement(measure, msrun_retention_time_p);
    }
  mpa_writer->endArray();
 
  mpa_writer->endMap();
}

References pappso::masschroq::PeptideMeasurementsBase::getMeasurementList(), and pappso::masschroq::MbrPeptideMeasurements::getPeptideSp().

writeMeasurement()

void pappso::masschroq::CborOutputStream::writeMeasurement ( const PeptideMeasurements::Measurement &  measurement, const pappso::MsRunRetentionTime< QString > *  msrun_retention_time_p  )

private

Definition at line 163 of file cboroutputstream.cpp.

{
 
  mpa_writer->startMap();
  mpa_writer->append(QLatin1String("charge"));
  mpa_writer->append(measurement.m_charge);
 
  mpa_writer->append(QLatin1String("mz"));
  mpa_writer->append(measurement.msp_xicCoord.get()->mzRange.getMz());
 
  if(m_isXicCoordOutput)
    {
      measurement.msp_xicCoord.get()->writeCborStream(*mpa_writer);
    }
 
  if(measurement.m_peptideNaturalIsotopeAverageSp.get() != nullptr)
    {
      mpa_writer->append(QLatin1String("isotope"));
      mpa_writer->append(measurement.m_peptideNaturalIsotopeAverageSp.get()->getIsotopeNumber());
 
      mpa_writer->append(QLatin1String("rank"));
      mpa_writer->append(measurement.m_peptideNaturalIsotopeAverageSp.get()->getIsotopeRank());
 
      mpa_writer->append(QLatin1String("th_ratio"));
      mpa_writer->append(measurement.m_peptideNaturalIsotopeAverageSp.get()->getIntensityRatio());
    }
 
 
  mpa_writer->append(QLatin1String("quality"));
  mpa_writer->append(pappso::masschroq::Utils::enumToString(measurement.m_peakQualityCategory));
 
  // label
  if(measurement.mp_peptideLabel != nullptr)
    {
      mpa_writer->append(QLatin1String("label"));
      mpa_writer->append(measurement.mp_peptideLabel->getLabel());
    }
 
  if(m_isTraceOutput && (measurement.msp_xicCoord.get()->xicSptr.get() != nullptr))
    {
      mpa_writer->append(QLatin1String("trace"));
      writeTrace(*(measurement.msp_xicCoord.get()->xicSptr.get()));
    }
 
 
  if(measurement.m_tracePeakSp.get() != nullptr)
    {
 
      if(m_isPeakShapeOutput && (measurement.msp_xicCoord.get()->xicSptr.get() != nullptr))
        {
 
          mpa_writer->append(QLatin1String("peak_shape"));
          mpa_writer->startMap();
          mpa_writer->append(QLatin1String("trace"));
 
          pappso::TraceSPtr trace_sp;
 
          pappso::FilterResampleKeepXRange cut_xic(
            measurement.m_tracePeakSp.get()->getLeftBoundary().x - m_peakShapeMarginInSeconds,
            measurement.m_tracePeakSp.get()->getRightBoundary().x + m_peakShapeMarginInSeconds);
 
          trace_sp = measurement.msp_xicCoord.get()->xicSptr;
          trace_sp.get()->filter(cut_xic);
 
 
          writeTrace(*(trace_sp.get()));
          mpa_writer->endMap();
        }
 
      mpa_writer->append(QLatin1String("peak"));
      writeTracePeak(*(measurement.m_tracePeakSp.get()), msrun_retention_time_p);
    }
  mpa_writer->endMap();
}

References pappso::masschroq::Utils::enumToString(), pappso::masschroq::PeptideLabel::getLabel(), pappso::masschroq::PeptideMeasurementsBase::Measurement::m_charge, pappso::masschroq::PeptideMeasurementsBase::Measurement::m_peakQualityCategory, pappso::masschroq::PeptideMeasurementsBase::Measurement::m_peptideNaturalIsotopeAverageSp, pappso::masschroq::PeptideMeasurementsBase::Measurement::m_tracePeakSp, pappso::masschroq::PeptideMeasurementsBase::Measurement::mp_peptideLabel, and pappso::masschroq::PeptideMeasurementsBase::Measurement::msp_xicCoord.

writeMsRun()

void pappso::masschroq::CborOutputStream::writeMsRun ( const MsRun &  msrun )

private

Definition at line 108 of file cboroutputstream.cpp.

{
  mpa_writer->append(QLatin1String("msrun"));
  mpa_writer->startMap(3);
  mpa_writer->append(QLatin1String("id"));
  mpa_writer->append(msrun.getMsRunReaderSPtr().get()->getMsRunId().get()->getXmlId());
  mpa_writer->append(QLatin1String("filename"));
  mpa_writer->append(msrun.getMsRunReaderSPtr().get()->getMsRunId().get()->getFileName());
  mpa_writer->append(QLatin1String("sample"));
  mpa_writer->append(msrun.getMsRunReaderSPtr().get()->getMsRunId().get()->getSampleName());
  mpa_writer->endMap();
}

References pappso::masschroq::MsRun::getMsRunReaderSPtr().

writeMsRunRetentionTime()

void pappso::masschroq::CborOutputStream::writeMsRunRetentionTime	(	const pappso::Trace &	report_common_ms2,
		const pappso::MsRunRetentionTime< QString > &	msrun_retention_time
	)

Definition at line 432 of file cboroutputstream.cpp.

{
  mpa_writer->startMap(5);
  mpa_writer->append(QLatin1String("original"));
  writeVectorDouble(msrun_retention_time.getMs1RetentionTimeVector());
  mpa_writer->append(QLatin1String("aligned"));
  writeVectorDouble(msrun_retention_time.getAlignedRetentionTimeVector());
  mpa_writer->append(QLatin1String("ms2_delta_rt"));
  writeTrace(report_common_ms2);
 
  pappso::Trace median(report_common_ms2);
  msrun_retention_time.getMs2MedianFilter().filter(median);
 
  mpa_writer->append(QLatin1String("ms2_median"));
  writeVectorDouble(median.yValues());
 
  msrun_retention_time.getMs2MeanFilter().filter(median);
  mpa_writer->append(QLatin1String("ms2_mean"));
  writeVectorDouble(median.yValues());
 
 
  mpa_writer->endMap();
}

References pappso::Trace::append(), pappso::FilterMorphoWindowBase::filter(), pappso::MsRunRetentionTime< T >::getAlignedRetentionTimeVector(), pappso::MsRunRetentionTime< T >::getMs1RetentionTimeVector(), pappso::MsRunRetentionTime< T >::getMs2MeanFilter(), pappso::MsRunRetentionTime< T >::getMs2MedianFilter(), and pappso::Trace::yValues().

Referenced by pappso::masschroq::MsRunGroup::alignRetentionTimeBetweenMsRuns().

writePeptideMeasurements()

void pappso::masschroq::CborOutputStream::writePeptideMeasurements ( const PeptideMeasurements &  peptide_measurements, const pappso::MsRunRetentionTime< QString > *  msrun_retention_time_p  )

private

Definition at line 123 of file cboroutputstream.cpp.

{
  pappso::masschroq::PeptideSp peptide_sp =
    peptide_measurements.getPeptideObservationSp().get()->getPeptideSp();
 
  mpa_writer->append(peptide_sp.get()->getId());
  mpa_writer->startMap();
  // mpa_writer->append(QLatin1String("peptide_id"));
  // mpa_writer->append(peptide_sp.get()->getId());
  mpa_writer->append(QLatin1String("proforma"));
  mpa_writer->append(peptide_sp.get()->getPappsoPeptideSp().get()->toProForma());
 
 
  mpa_writer->append(QLatin1String("mods"));
  mpa_writer->append(peptide_sp.get()->getMods());
 
  std::size_t size_measurement = peptide_measurements.getMeasurementList().size();
  if(size_measurement > 0)
    {
      mpa_writer->append(QLatin1String("rt_target"));
      mpa_writer->append(
        peptide_measurements.getMeasurementList().at(0).msp_xicCoord.get()->rtTarget);
    }
 
  mpa_writer->append(QLatin1String("xics"));
  mpa_writer->startArray(size_measurement);
  for(const pappso::masschroq::PeptideMeasurements::Measurement &measure :
      peptide_measurements.getMeasurementList())
    {
      // write(peptide_sp, measure, msrun_retention_time_p);
      writeMeasurement(measure, msrun_retention_time_p);
    }
  mpa_writer->endArray();
 
  mpa_writer->endMap();
}

References pappso::masschroq::PeptideMeasurementsBase::getMeasurementList(), and pappso::masschroq::PeptideMeasurements::getPeptideObservationSp().

writeProjectParameters()

void pappso::masschroq::CborOutputStream::writeProjectParameters

(

const pappso::ProjectParameters &

project_parameters

)

Definition at line 425 of file cboroutputstream.cpp.

{
  project_parameters.writeParameters(*mpa_writer);
}

References pappso::ProjectParameters::writeParameters().

Referenced by pappso::masschroq::JsonInput::action().

writeQrDataBlock()

void pappso::masschroq::CborOutputStream::writeQrDataBlock	(	pappso::UiMonitorInterface &	m_uiMonitor,
		const MsRunPeptideList &	msrun_peptide_list,
		bool	is_mbr
	)

Definition at line 338 of file cboroutputstream.cpp.

{
 
  quint64 size;
  if(is_mbr)
    {
      size = msrun_peptide_list.getMbrPeptideMeasurementsList().size();
 
      monitor.setStatus(QString("Writing MBR quantification results for msrun %1")
                          .arg(msrun_peptide_list.getMsRunSp()
                                 .get()
                                 ->getMsRunReaderSPtr()
                                 .get()
                                 ->getMsRunId()
                                 .get()
                                 ->getSampleName()));
    }
  else
    {
      size = msrun_peptide_list.getPeptideMeasurementsList().size();
 
      monitor.setStatus(QString("Writing quantification results for msrun %1")
                          .arg(msrun_peptide_list.getMsRunSp()
                                 .get()
                                 ->getMsRunReaderSPtr()
                                 .get()
                                 ->getMsRunId()
                                 .get()
                                 ->getSampleName()));
    }
  monitor.setTotalSteps(size);
  mpa_writer->append(msrun_peptide_list.getMsRunSp()
                       .get()
                       ->getMsRunReaderSPtr()
                       .get()
                       ->getMsRunId()
                       .get()
                       ->getXmlId());
  mpa_writer->startMap();
  writeMsRun(*(msrun_peptide_list.getMsRunSp().get()));
 
 
  mpa_writer->append("peptide_measurements");
  mpa_writer->startMap(size);
  if(is_mbr)
    {
      for(const pappso::masschroq::MbrPeptideMeasurementsSp &measures :
          msrun_peptide_list.getMbrPeptideMeasurementsList())
        {
          writeMbrPeptideMeasurements(*(measures.get()),
                                      msrun_peptide_list.getMsRunRetentionTimeConstPtr());
 
          monitor.count();
        }
    }
  else
    {
      for(const pappso::masschroq::PeptideMeasurementsSp &measures :
          msrun_peptide_list.getPeptideMeasurementsList())
        {
          writePeptideMeasurements(*(measures.get()),
                                   msrun_peptide_list.getMsRunRetentionTimeConstPtr());
 
          monitor.count();
        }
    }
  monitor.setTotalSteps(0);
  mpa_writer->endMap();
 
  mpa_writer->endMap();
}

References pappso::UiMonitorInterface::count(), pappso::masschroq::MsRunPeptideList::getMbrPeptideMeasurementsList(), pappso::masschroq::MsRunPeptideList::getMsRunRetentionTimeConstPtr(), pappso::masschroq::MsRunPeptideList::getMsRunSp(), pappso::masschroq::MsRunPeptideList::getPeptideMeasurementsList(), pappso::UiMonitorInterface::setStatus(), and pappso::UiMonitorInterface::setTotalSteps().

Referenced by pappso::masschroq::MsRunGroup::quantify().

writeTrace()

void pappso::masschroq::CborOutputStream::writeTrace ( const pappso::Trace &  trace )

private

Definition at line 242 of file cboroutputstream.cpp.

{
  mpa_writer->startMap(2);
  mpa_writer->append(QLatin1String("x"));
  mpa_writer->startArray(trace.size());
  for(double x : trace.xValues())
    {
      mpa_writer->append(x);
    }
  mpa_writer->endArray();
 
 
  mpa_writer->append(QLatin1String("y"));
  mpa_writer->startArray(trace.size());
  for(double y : trace.yValues())
    {
      mpa_writer->append(y);
    }
  mpa_writer->endArray();
  mpa_writer->endMap();
}

References pappso::x, pappso::Trace::xValues(), pappso::y, and pappso::Trace::yValues().

writeTracePeak()

void pappso::masschroq::CborOutputStream::writeTracePeak ( const pappso::TracePeak &  peak, const pappso::MsRunRetentionTime< QString > *  msrun_retention_time_p  )

private

Definition at line 265 of file cboroutputstream.cpp.

{
  mpa_writer->startMap();
  mpa_writer->append(QLatin1String("area"));
  mpa_writer->append(peak.getArea());
 
  mpa_writer->append(QLatin1String("max_intensity"));
  mpa_writer->append(peak.getMaxXicElement().y);
 
  mpa_writer->append(QLatin1String("rt"));
  mpa_writer->startArray();
  mpa_writer->append(peak.getLeftBoundary().x);
  mpa_writer->append(peak.getMaxXicElement().x);
  mpa_writer->append(peak.getRightBoundary().x);
  mpa_writer->endArray();
 
  if((msrun_retention_time_p != nullptr) && msrun_retention_time_p->isAligned())
    {
      mpa_writer->append(QLatin1String("aligned_rt"));
      mpa_writer->startArray();
      mpa_writer->append(
        msrun_retention_time_p->translateOriginal2AlignedRetentionTime(peak.getLeftBoundary().x));
      mpa_writer->append(
        msrun_retention_time_p->translateOriginal2AlignedRetentionTime(peak.getMaxXicElement().x));
      mpa_writer->append(
        msrun_retention_time_p->translateOriginal2AlignedRetentionTime(peak.getRightBoundary().x));
      mpa_writer->endArray();
    }
 
  mpa_writer->endMap();
}

References pappso::TracePeak::getArea(), pappso::TracePeak::getLeftBoundary(), pappso::TracePeak::getMaxXicElement(), pappso::TracePeak::getRightBoundary(), pappso::MsRunRetentionTime< T >::isAligned(), pappso::MsRunRetentionTime< T >::translateOriginal2AlignedRetentionTime(), pappso::DataPoint::x, and pappso::DataPoint::y.

writeVectorDouble()

void pappso::masschroq::CborOutputStream::writeVectorDouble ( const std::vector< double > &  vector )

private

Definition at line 414 of file cboroutputstream.cpp.

{
  mpa_writer->startArray(vector.size());
  for(double x : vector)
    {
      mpa_writer->append(x);
    }
  mpa_writer->endArray();
}

References pappso::x.

Member Data Documentation

m_isPeakShapeOutput

bool pappso::masschroq::CborOutputStream::m_isPeakShapeOutput = false

private

Definition at line 115 of file cboroutputstream.h.

m_isTraceOutput

bool pappso::masschroq::CborOutputStream::m_isTraceOutput = false

private

Definition at line 114 of file cboroutputstream.h.

m_isXicCoordOutput

bool pappso::masschroq::CborOutputStream::m_isXicCoordOutput = true

private

Definition at line 116 of file cboroutputstream.h.

m_peakShapeMarginInSeconds

double pappso::masschroq::CborOutputStream::m_peakShapeMarginInSeconds = 20

private

Definition at line 118 of file cboroutputstream.h.

mpa_writer

pappso::cbor::CborStreamWriter* pappso::masschroq::CborOutputStream::mpa_writer = nullptr

private

Definition at line 113 of file cboroutputstream.h.

Referenced by CborOutputStream().

---

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

• pappsomspp/masschroq/output/cboroutputstream.h
• pappsomspp/masschroq/output/cboroutputstream.cpp