OnDiscMSExperiment.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/INTERFACES/DataStructures.h>
 
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
#include <OpenMS/METADATA/ExperimentalSettings.h>
#include <OpenMS/FORMAT/HANDLERS/IndexedMzMLHandler.h>
 
 
#include <vector>
#include <algorithm>
#include <limits>
 
#include <boost/shared_ptr.hpp>
 
namespace OpenMS
{
  class OPENMS_DLLAPI OnDiscMSExperiment
  {
 
  typedef ChromatogramPeak ChromatogramPeakT;
  typedef Peak1D PeakT;
 
public:
 
    OnDiscMSExperiment() {}
 
    bool openFile(const String& filename, bool skipMetaData = false)
    {
      filename_ = filename;
      indexed_mzml_file_.openFile(filename);
      if (filename != "" && !skipMetaData)
      {
        loadMetaData_(filename);
      }
      return indexed_mzml_file_.getParsingSuccess();
    }
 
    OnDiscMSExperiment(const OnDiscMSExperiment& source) :
      filename_(source.filename_),
      indexed_mzml_file_(source.indexed_mzml_file_),
      meta_ms_experiment_(source.meta_ms_experiment_)
    {
    }
 
    bool operator==(const OnDiscMSExperiment& rhs) const
    {
      if (meta_ms_experiment_ == nullptr || rhs.meta_ms_experiment_ == nullptr) 
      {
        return filename_ == rhs.filename_ &&
               meta_ms_experiment_ == rhs.meta_ms_experiment_;
      }
 
      // check if file and meta information is the same
      return filename_ == rhs.filename_ &&
             (*meta_ms_experiment_) == (*rhs.meta_ms_experiment_);
      // do not check if indexed_mzml_file_ is equal -> they have the same filename...
    }
 
    bool operator!=(const OnDiscMSExperiment& rhs) const
    {
      return !(operator==(rhs));
    }
 
    bool isSortedByRT() const
    {
      if (!meta_ms_experiment_) return false;
 
      return meta_ms_experiment_->isSorted(false);
    }
 
    inline Size size() const
    {
      return getNrSpectra();
    }
 
    inline bool empty() const
    {
      return indexed_mzml_file_.getNrSpectra() == 0;
    }
 
    inline Size getNrSpectra() const
    {
      return indexed_mzml_file_.getNrSpectra();
    }
 
    inline Size getNrChromatograms() const
    {
      return indexed_mzml_file_.getNrChromatograms();
    }
 
    boost::shared_ptr<const ExperimentalSettings> getExperimentalSettings() const
    {
      return boost::static_pointer_cast<const ExperimentalSettings>(meta_ms_experiment_);
    }
 
    boost::shared_ptr<PeakMap> getMetaData() const
    {
      return meta_ms_experiment_;
    }
 
    inline MSSpectrum operator[](Size n)
    {
      return getSpectrum(n);
    }
 
    MSSpectrum getSpectrum(Size id)
    {
      if (!meta_ms_experiment_) return indexed_mzml_file_.getMSSpectrumById(int(id));
 
      MSSpectrum spectrum(meta_ms_experiment_->operator[](id));
      indexed_mzml_file_.getMSSpectrumById(int(id), spectrum);
      return spectrum;
    }
 
    OpenMS::Interfaces::SpectrumPtr getSpectrumById(Size id)
    {
      return indexed_mzml_file_.getSpectrumById((int)id);
    }
 
    MSChromatogram getChromatogram(Size id)
    {
      if (!meta_ms_experiment_) return indexed_mzml_file_.getMSChromatogramById(int(id));
 
      MSChromatogram chromatogram(meta_ms_experiment_->getChromatogram(id));
      indexed_mzml_file_.getMSChromatogramById(int(id), chromatogram);
      return chromatogram;
    }
 
    MSChromatogram getChromatogramByNativeId(const std::string& id);
 
    MSSpectrum getSpectrumByNativeId(const std::string& id);
 
    OpenMS::Interfaces::ChromatogramPtr getChromatogramById(Size id)
    {
      return indexed_mzml_file_.getChromatogramById(id);
    }
 
    void setSkipXMLChecks(bool skip)
    {
      indexed_mzml_file_.setSkipXMLChecks(skip);
    }
 
private:
 
    OnDiscMSExperiment& operator=(const OnDiscMSExperiment& /* source */);
 
    void loadMetaData_(const String& filename);
 
    MSChromatogram getMetaChromatogramById_(const std::string& id);
 
    MSSpectrum getMetaSpectrumById_(const std::string& id);
 
protected:
 
    String filename_;
    Internal::IndexedMzMLHandler indexed_mzml_file_;
    boost::shared_ptr<PeakMap> meta_ms_experiment_;
    std::unordered_map< std::string, Size > chromatograms_native_ids_;
    std::unordered_map< std::string, Size > spectra_native_ids_;
  };
 
typedef OpenMS::OnDiscMSExperiment OnDiscPeakMap;
 
} // namespace OpenMS