msrunxicextractor.cpp

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/**
 * \file pappsomspp/xicextractor/private/msrunxicextractorpwiz.cpp
 * \date 07/05/2018
 * \author Olivier Langella
 * \brief simple proteowizard based XIC extractor
 */
 
/*******************************************************************************
 * Copyright (c) 2018 Olivier Langella <Olivier.Langella@u-psud.fr>.
 *
 * This file is part of the PAPPSOms++ library.
 *
 *     PAPPSOms++ 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.
 *
 *     PAPPSOms++ 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 PAPPSOms++.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
 *     Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
 *implementation
 ******************************************************************************/
 
#include "msrunxicextractor.h"
#include <QDebug>
#include <QObject>
 
#include "pappsomspp/core/pappsoexception.h"
#include "pappsomspp/core/exception/exceptioninterrupted.h"
#include "pappsomspp/core/processing/filters/filterresample.h"
 
namespace pappso
{
 
 
MsRunXicExtractor::MsRunXicExtractor(MsRunReaderSPtr &msrun_reader)
  : pappso::MsRunXicExtractorInterface(msrun_reader)
{
 
  MsRunXicExtractorReadPoints get_msrun_points(m_msrun_points);
 
 
  pappso::MsRunReadConfig config;
  config.setNeedPeakList(true);
  config.setMsLevels({1});
 
  msp_msrun_reader.get()->readSpectrumCollection2(config, get_msrun_points);
 
  std::sort(
    m_msrun_points.begin(),
    m_msrun_points.end(),
    [](const MsRunXicExtractorPoints &a, const MsRunXicExtractorPoints &b) { return a.rt < b.rt; });
 
 
  if(m_msrun_points.size() == 0)
    {
      throw pappso::PappsoException(
        QObject::tr("error extracting XIC: no MS level 1 in data file"));
    }
}
MsRunXicExtractor::~MsRunXicExtractor()
{
}
 
 
MsRunXicExtractor::MsRunXicExtractor(const MsRunXicExtractor &other)
  : MsRunXicExtractorInterface(other)
{
  m_msrun_points = other.m_msrun_points;
}
 
 
void
MsRunXicExtractor::protectedExtractXicCoordSPtrList(
  UiMonitorInterface &monitor,
  std::vector<XicCoordSPtr>::iterator it_xic_coord_list_begin,
  std::vector<XicCoordSPtr>::iterator it_xic_coord_list_end)
{
 
  // sort xic by mz:
  std::sort(it_xic_coord_list_begin, it_xic_coord_list_end, [](XicCoordSPtr &a, XicCoordSPtr &b) {
    return a.get()->rtTarget < b.get()->rtTarget;
  });
 
  for(auto it = it_xic_coord_list_begin; it != it_xic_coord_list_end; it++)
    {
      // XicCoord *p_xic_coord = sp_xic_coord.get();
      extractOneXicCoord(*(it->get()));
      monitor.count();
      if(monitor.shouldIstop())
        {
          throw pappso::ExceptionInterrupted(QObject::tr("Xic extraction process interrupted"));
        }
    }
}
 
 
void
MsRunXicExtractor::extractOneXicCoord(XicCoord &xic_coord)
{
  FilterResampleKeepXRange keep_range(xic_coord.mzRange.lower(), xic_coord.mzRange.upper());
  std::shared_ptr<Xic> msrunxic_sp = xic_coord.xicSptr;
 
  double rt_begin = xic_coord.rtTarget - m_retentionTimeAroundTarget;
  double rt_end   = xic_coord.rtTarget + m_retentionTimeAroundTarget;
 
 
  auto itpoints = m_msrun_points.begin();
 
  // find startint retention time :
  while((itpoints != m_msrun_points.end()) && (itpoints->rt < rt_begin))
    {
      itpoints++;
    }
  MassSpectrumSPtr spectrum;
  DataPoint peak;
  while((itpoints != m_msrun_points.end()) && (itpoints->rt <= rt_end))
    {
      spectrum = msp_msrun_reader.get()->massSpectrumSPtr(itpoints->spectrum_index);
      // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
      // << spectrum->size(); spectrum->debugPrintValues();
 
      qDebug() << " spectrum->size()=" << spectrum->size();
      keep_range.filter(*(spectrum.get()));
      qDebug() << " spectrum->size()=" << spectrum->size();
 
      peak.x = itpoints->rt;
 
      if(m_xicExtractMethod == Enums::XicExtractMethod::max)
        {
          peak.y = 0;
          if(spectrum->size() > 0)
            {
              peak.y = maxYDataPoint(spectrum->begin(), spectrum->end())->y;
 
              qDebug() << " peak.y=" << peak.y << " spectrum->size()=" << spectrum->size();
            }
        }
      else
        {
          peak.y = sumYTrace(spectrum->begin(), spectrum->end(), 0);
        }
      msrunxic_sp->push_back(peak);
 
      itpoints++;
    }
}
 
} // namespace pappso