msrunxicextractorfactory.cpp

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/**
 * \file pappsomspp/xicextractor/msrunxicextractorfactory.cpp
 * \date 07/05/2018
 * \author Olivier Langella
 * \brief factory to build XIC extractor on an MsRun file
 */
 
/*******************************************************************************
 * 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 "msrunxicextractorfactory.h"
#include "private/msrunxicextractor.h"
#include "private/msrunxicextractordisk.h"
#include "private/msrunxicextractordiskbuffer.h"
#include "pappsomspp/core/vendors/tims/xicextractor/timsdirectxicextractor.h"
#include "pappsomspp/core/msrun/private/timsmsrunreaderms2.h"
 
namespace pappso
{
 
 
MsRunXicExtractorFactory MsRunXicExtractorFactory::m_instance =
  MsRunXicExtractorFactory();
 
MsRunXicExtractorFactory &
MsRunXicExtractorFactory::getInstance()
{
  return m_instance;
}
 
 
MsRunXicExtractorFactory::MsRunXicExtractorFactory()
{
}
MsRunXicExtractorFactory::~MsRunXicExtractorFactory()
{
}
 
void
MsRunXicExtractorFactory::setTmpDir(const QString &dir_name)
{
  m_tmpDirName = dir_name;
}
void
MsRunXicExtractorFactory::setMsRunXicExtractorFactoryType(
  pappso::MsRunXicExtractorFactoryType type)
{
  m_type = type;
}
 
MsRunXicExtractorInterfaceSp
MsRunXicExtractorFactory::buildMsRunXicExtractorSp(
  MsRunReaderSPtr &msrun_reader) const
{
 
  pappso::TimsMsRunReaderMs2 *tims2_reader =
    dynamic_cast<pappso::TimsMsRunReaderMs2 *>(msrun_reader.get());
  if(tims2_reader == nullptr)
    {
      // NO TIMS
      if((m_type == MsRunXicExtractorFactoryType::nose) ||
         (m_type == MsRunXicExtractorFactoryType::direct))
        {
          std::shared_ptr<MsRunXicExtractor> msrun_xic_extractor_sp =
            std::make_shared<MsRunXicExtractor>(
              MsRunXicExtractor(msrun_reader));
          return (msrun_xic_extractor_sp);
        }
      else if(m_type == MsRunXicExtractorFactoryType::disk)
        {
 
          std::shared_ptr<MsRunXicExtractorDisk> msrun_xic_extractor_sp =
            std::make_shared<MsRunXicExtractorDisk>(
              MsRunXicExtractorDisk(msrun_reader, QDir(m_tmpDirName)));
 
          msrun_xic_extractor_sp.get()->prepareExtractor();
          return (msrun_xic_extractor_sp);
        }
      else if(m_type == MsRunXicExtractorFactoryType::diskbuffer)
        {
 
          std::shared_ptr<MsRunXicExtractorDiskBuffer> msrun_xic_extractor_sp =
            std::make_shared<MsRunXicExtractorDiskBuffer>(
              MsRunXicExtractorDiskBuffer(msrun_reader, QDir(m_tmpDirName)));
          msrun_xic_extractor_sp.get()->prepareExtractor();
          return (msrun_xic_extractor_sp);
        }
    }
  else
    {
      // TIMS
      std::shared_ptr<TimsDirectXicExtractor> msrun_xic_extractor_sp =
        std::make_shared<TimsDirectXicExtractor>(msrun_reader);
      return (msrun_xic_extractor_sp);
    }
  return nullptr;
}
 
 
} // namespace pappso