cboroutputstream.cpp

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/**
 * \file pappsomspp/masschroq/output/cboroutputstream.cpp
 * \date 02/01/2025
 * \author Olivier Langella
 * \brief quantification result cbor writer for MassChroqLight
 */
 
/*******************************************************************************
 * Copyright (c) 2025 Olivier Langella
 *<Olivier.Langella@universite-paris-saclay.fr>.
 *
 * This file is part of MassChroQ.
 *
 *     MassChroQ is free software: you can redistribute it and/or modify
 *     it under the terms of the GNU General Public License as published by
 *     the Free Software Foundation, either version 3 of the License, or
 *     (at your option) any later version.
 *
 *     MassChroQ is distributed in the hope that it will be useful,
 *     but WITHOUT ANY WARRANTY; without even the implied warranty of
 *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *     GNU General Public License for more details.
 *
 *     You should have received a copy of the GNU General Public License
 *     along with MassChroQ.  If not, see <http://www.gnu.org/licenses/>.
 *
 ******************************************************************************/
 
#include "cboroutputstream.h"
#include <QDateTime>
#include <QCborMap>
#include <QThreadPool>
#include "../peptide.h"
#include "../peptideobservation.h"
#include "../utils.h"
#include "../../utils.h"
#include "../../processing/filters/filterresample.h"
 
pappso::masschroq::CborOutputStream::CborOutputStream(QIODevice *device)
{
  mpa_writer = new pappso::cbor::CborStreamWriter(device);
  mpa_writer->startMap();
}
 
pappso::masschroq::CborOutputStream::~CborOutputStream()
{
}
 
void
pappso::masschroq::CborOutputStream::setIsPeakShapeOutput(bool is_shape_output,
                                                          double margin_in_seconds)
{
  m_isPeakShapeOutput        = is_shape_output;
  m_peakShapeMarginInSeconds = margin_in_seconds;
}
 
void
pappso::masschroq::CborOutputStream::setIsTraceOutput(bool is_trace_output)
{
  m_isTraceOutput = is_trace_output;
}
 
void
pappso::masschroq::CborOutputStream::writeActionBegin(const QString &operation)
{
  mpa_writer->writeInformations(
    "masschroq", pappso::masschroq::Utils::getVersion(), "quantification", "quantification");
}
 
 
void
pappso::masschroq::CborOutputStream::writeActionEnd()
{
  mpa_writer->append(QLatin1String("end"));
  mpa_writer->startMap();
  mpa_writer->append(QLatin1String("timestamp"));
  mpa_writer->append(QDateTime::currentDateTime().toString(Qt::ISODate));
  mpa_writer->endMap();
}
void
pappso::masschroq::CborOutputStream::close()
{
  writeActionEnd();
  mpa_writer->endMap();
 
  delete mpa_writer;
}
 
void
pappso::masschroq::CborOutputStream::writeJsonObject(const QString &name,
                                                     const QJsonObject &json_object)
{
  mpa_writer->append(name);
  QCborMap map;
  map = map.fromJsonObject(json_object);
  map.toCborValue().toCbor(*mpa_writer);
}
 
QCborStreamWriter &
pappso::masschroq::CborOutputStream::getCborStreamWriter()
{
  return (*mpa_writer);
}
 
 
void
pappso::masschroq::CborOutputStream::writeMsRun(const pappso::masschroq::MsRun &msrun)
{
  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();
}
 
 
void
pappso::masschroq::CborOutputStream::writePeptideMeasurements(
  const pappso::masschroq::PeptideMeasurements &peptide_measurements,
  const pappso::MsRunRetentionTime<QString> *msrun_retention_time_p)
{
  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();
}
 
void
pappso::masschroq::CborOutputStream::writeMeasurement(
  const pappso::masschroq::PeptideMeasurements::Measurement &measurement,
  const pappso::MsRunRetentionTime<QString> *msrun_retention_time_p)
{
 
  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();
}
 
 
void
pappso::masschroq::CborOutputStream::writeTrace(const pappso::Trace &trace)
{
  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();
}
 
void
pappso::masschroq::CborOutputStream::writeTracePeak(
  const pappso::TracePeak &peak, const pappso::MsRunRetentionTime<QString> *msrun_retention_time_p)
{
  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();
}
 
 
void
pappso::masschroq::CborOutputStream::writeMbrPeptideMeasurements(
  const pappso::masschroq::MbrPeptideMeasurements &mbr_peptide_measurements,
  const pappso::MsRunRetentionTime<QString> *msrun_retention_time_p)
{
  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();
}
 
void
pappso::masschroq::CborOutputStream::writeQrDataBlock(
  pappso::UiMonitorInterface &monitor,
  const pappso::masschroq::MsRunPeptideList &msrun_peptide_list,
  bool is_mbr)
{
 
  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();
}
 
void
pappso::masschroq::CborOutputStream::writeVectorDouble(const std::vector<double> &vector)
{
  mpa_writer->startArray(vector.size());
  for(double x : vector)
    {
      mpa_writer->append(x);
    }
  mpa_writer->endArray();
}
 
void
pappso::masschroq::CborOutputStream::writeProjectParameters(
  const pappso::ProjectParameters &project_parameters)
{
  project_parameters.writeParameters(*mpa_writer);
}
 
void
pappso::masschroq::CborOutputStream::writeMsRunRetentionTime(
  const pappso::Trace &report_common_ms2,
  const pappso::MsRunRetentionTime<QString> &msrun_retention_time)
{
  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();
}