IndexedMzMLFileLoader.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry               
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/KERNEL/OnDiscMSExperiment.h>
#include <OpenMS/FORMAT/DATAACCESS/MSDataWritingConsumer.h>

namespace OpenMS
{

  class OPENMS_DLLAPI IndexedMzMLFileLoader
  {
    public:

    IndexedMzMLFileLoader();

    ~IndexedMzMLFileLoader();

    PeakFileOptions& getOptions();

    const PeakFileOptions& getOptions() const;

    void setOptions(const PeakFileOptions &);

    bool load(const String& filename, OnDiscPeakMap& exp)
    {
      return exp.openFile(filename);
    }

    void store(const String& filename, OnDiscPeakMap& exp)
    {
      // Create a writing data consumer which consumes the experiment (writes it to disk)
      PlainMSDataWritingConsumer consumer(filename);
      consumer.setExpectedSize(exp.getNrSpectra(), exp.getNrChromatograms());
      consumer.setExperimentalSettings(*exp.getExperimentalSettings().get());
      options_.setWriteIndex(true);  // ensure that we write the index
      consumer.setOptions(options_);
      for (Size i = 0; i < exp.getNrSpectra(); i++)
      {
        MSSpectrum s = exp.getSpectrum(i);
        consumer.consumeSpectrum(s);
      }
      for (Size i = 0; i < exp.getNrChromatograms(); i++)
      {
        MSChromatogram c = exp.getChromatogram(i);
        consumer.consumeChromatogram(c);
      }
    }

    void store(const String& filename, PeakMap& exp)
    {
      MzMLFile f;
      options_.setWriteIndex(true);  // ensure that we write the index
      f.setOptions(options_);
      f.store(filename, exp);
    }

private:

    PeakFileOptions options_;

  };
}