timsdirectxicextractor.cpp

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/**
 * \file pappsomspp/vendors/tims/xicextractor/timsdirectxicextractor.cpp
 * \date 21/09/2019
 * \author Olivier Langella
 * \brief minimum functions to extract XICs from Tims Data
 */
 
/*******************************************************************************
 * Copyright (c) 2019 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/>.
 *
 ******************************************************************************/
 
#include "timsdirectxicextractor.h"
#include <QDebug>
 
using namespace pappso;
 
TimsDirectXicExtractor::TimsDirectXicExtractor(const TimsData *mp_tims_data)
  : pappso::TimsXicExtractorInterface(mp_tims_data)
{
}
 
TimsDirectXicExtractor::~TimsDirectXicExtractor()
{
}
 
 
void
TimsDirectXicExtractor::extractTimsXicList(
  std::vector<TimsXicStructure> &timsXicList, double rtRange) const
{
  qDebug();
  if(timsXicList.size() == 0)
    return;
  std::sort(timsXicList.begin(),
            timsXicList.end(),
            [](const TimsXicStructure &a, const TimsXicStructure &b) {
              return a.rtTarget < b.rtTarget;
            });
 
  std::vector<std::size_t> tims_frameid_list =
    mp_timsData->getTimsMS1FrameIdRange(timsXicList[0].rtTarget - rtRange,
                                        timsXicList.back().rtTarget + rtRange);
 
  qDebug() << " tims_frameid_list.size()=" << tims_frameid_list.size();
  qDebug() << " rt begin=" << timsXicList[0].rtTarget;
  qDebug() << " rt end=" << timsXicList.back().rtTarget;
  for(std::size_t frame_id : tims_frameid_list)
    {
      std::vector<TimsXicStructure>::iterator itXicListbegin =
        timsXicList.begin();
      std::vector<TimsXicStructure>::iterator itXicListend = timsXicList.end();
      TimsFrameCstSPtr frame_sptr = mp_timsData->getTimsFrameCstSPtr(frame_id);
      double rtframe              = frame_sptr.get()->getTime();
 
      double rtbeginframe = rtframe - rtRange;
      double rtendframe   = rtframe + rtRange;
 
      while((itXicListbegin != itXicListend) &&
            (itXicListbegin->rtTarget < rtbeginframe))
        {
          itXicListbegin++;
        }
      itXicListend = itXicListbegin;
      while((itXicListend != timsXicList.end()) &&
            (itXicListend->rtTarget < rtendframe))
        {
          itXicListend++;
        }
      /*
      while((itXicListbegin != timsXicList.end()) &&
            ((itXicListbegin->rtTarget + rtRange) < rtframe))
        {
 
          qDebug() << " itXicListbegin->rtTarget + rtRange="
                   << itXicListbegin->rtTarget + rtRange
                   << " rtframe=" << rtframe;
          itXicListbegin++;
        }
*/
      qDebug() << " from=" << itXicListbegin->rtTarget
               << " to=" << itXicListend->rtTarget;
      frame_sptr.get()->extractTimsXicListInRtRange(
        itXicListbegin, itXicListend, m_xicExtractMethod);
    }
  qDebug();
}