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 2002-2017.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------

#ifndef OPENMS_KERNEL_ONDISCMSEXPERIMENT_H
#define OPENMS_KERNEL_ONDISCMSEXPERIMENT_H

#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/IndexedMzMLFile.h>
#include <OpenMS/FORMAT/MzMLFile.h>

#include <vector>
#include <algorithm>
#include <limits>

#include <boost/shared_ptr.hpp>

namespace OpenMS
{
  class 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
    {
      // 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
    {
      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_);
    }

    inline MSSpectrum operator[](Size n)
    {
      return getSpectrum(n);
    }

    MSSpectrum getSpectrum(Size id)
    {
      OpenMS::Interfaces::SpectrumPtr sptr = indexed_mzml_file_.getSpectrumById(static_cast<int>(id));
      MSSpectrum spectrum(meta_ms_experiment_->operator[](id));

      // recreate a spectrum from the data arrays!
      OpenMS::Interfaces::BinaryDataArrayPtr mz_arr = sptr->getMZArray();
      OpenMS::Interfaces::BinaryDataArrayPtr int_arr = sptr->getIntensityArray();
      spectrum.reserve(mz_arr->data.size());
      for (Size i = 0; i < mz_arr->data.size(); i++)
      {
        PeakT p;
        p.setMZ(mz_arr->data[i]);
        p.setIntensity(int_arr->data[i]);
        spectrum.push_back(p);
      }
      return spectrum;
    }

    OpenMS::Interfaces::SpectrumPtr getSpectrumById(Size id)
    {
      return indexed_mzml_file_.getSpectrumById(id);
    }

    MSChromatogram getChromatogram(Size id)
    {
      OpenMS::Interfaces::ChromatogramPtr cptr = indexed_mzml_file_.getChromatogramById(static_cast<int>(id));
      MSChromatogram chromatogram(meta_ms_experiment_->getChromatogram(id));

      // recreate a chromatogram from the data arrays!
      OpenMS::Interfaces::BinaryDataArrayPtr rt_arr = cptr->getTimeArray();
      OpenMS::Interfaces::BinaryDataArrayPtr int_arr = cptr->getIntensityArray();
      chromatogram.reserve(rt_arr->data.size());
      for (Size i = 0; i < rt_arr->data.size(); i++)
      {
        ChromatogramPeakT p;
        p.setRT(rt_arr->data[i]);
        p.setIntensity(int_arr->data[i]);
        chromatogram.push_back(p);
      }

      return chromatogram;
    }

    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)
    {
      meta_ms_experiment_ = boost::shared_ptr< PeakMap >(new PeakMap);

      MzMLFile f;
      PeakFileOptions options = f.getOptions();
      options.setFillData(false);
      f.setOptions(options);
      f.load(filename, *meta_ms_experiment_.get());
    }


protected:

    String filename_;
    IndexedMzMLFile indexed_mzml_file_;
    boost::shared_ptr<PeakMap> meta_ms_experiment_;
  };

typedef OpenMS::OnDiscMSExperiment OnDiscPeakMap;

} // namespace OpenMS

#endif // OPENMS_KERNEL_ONDISCMSEXPERIMENT_H