LayerStoreData.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
// This software is released under a three-clause BSD license:
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//  * 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.
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//    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.
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// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

// OpenMS_GUI config

#include <OpenMS/FILTERING/DATAREDUCTION/DataFilters.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/RangeManager.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/VISUAL/INTERFACES/IPeptideIds.h>


namespace OpenMS
{

  class OPENMS_GUI_DLLAPI LayerStoreData
  {
  public:
    LayerStoreData(FileTypeList supported_storage_formats) :
        storage_formats_(supported_storage_formats)
    {
    }

    virtual ~LayerStoreData() = default;

    FileTypeList getSupportedFileFormats() const
    {
      return storage_formats_;
    }

    virtual void saveToFile(const String& filename, const ProgressLogger::LogType lt) const = 0;

  protected:

    FileTypes::Type getSupportedExtension_(const String& filename) const;

    FileTypeList storage_formats_; 
  };

  class OPENMS_GUI_DLLAPI LayerStoreDataPeakMapVisible
   : public LayerStoreData
  {
  public:
    LayerStoreDataPeakMapVisible() :
      LayerStoreData(FileTypeList({FileTypes::MZML, FileTypes::MZDATA, FileTypes::MZXML}))
    {}

    // docu in base class
    void saveToFile(const String& filename, const ProgressLogger::LogType lt) const override;

    void storeVisibleSpectrum(const MSSpectrum& spec, const RangeAllType& visible_range, const DataFilters& layer_filters);
    void storeVisibleChromatogram(const MSChromatogram& chrom, const RangeAllType& visible_range, const DataFilters& layer_filters);

    void storeVisibleExperiment(const PeakMap& exp, const RangeAllType& visible_range, const DataFilters& layer_filters);

  private:
    PeakMap pm_; 
  };

  class OPENMS_GUI_DLLAPI LayerStoreDataPeakMapAll : public LayerStoreData
  {
  public:
    LayerStoreDataPeakMapAll() : LayerStoreData(FileTypeList({FileTypes::MZML, FileTypes::MZDATA, FileTypes::MZXML}))
    {
    }

    // docu in base class
    void saveToFile(const String& filename, const ProgressLogger::LogType lt) const override;

    void storeFullExperiment(const PeakMap& exp);

  private:
    const PeakMap* full_exp_ = nullptr; 
  };

  class OPENMS_GUI_DLLAPI LayerStoreDataFeatureMapVisible : public LayerStoreData
  {
  public:
    LayerStoreDataFeatureMapVisible() : LayerStoreData(FileTypeList({FileTypes::FEATUREXML}))
    {
    }

    // docu in base class
    void saveToFile(const String& filename, const ProgressLogger::LogType lt) const override;

    void storeVisibleFM(const FeatureMap& fm, const RangeAllType& visible_range, const DataFilters& layer_filters);

  private:
    FeatureMap fm_; 
  };

  class OPENMS_GUI_DLLAPI LayerStoreDataFeatureMapAll : public LayerStoreData
  {
  public:
    LayerStoreDataFeatureMapAll() : LayerStoreData(FileTypeList({FileTypes::FEATUREXML}))
    {
    }

    // docu in base class
    void saveToFile(const String& filename, const ProgressLogger::LogType lt) const override;

    void storeFullFM(const FeatureMap& fm);

  private:
    const FeatureMap* full_fm_ = nullptr; 
  };

  class OPENMS_GUI_DLLAPI LayerStoreDataConsensusMapVisible : public LayerStoreData
  {
  public:
    LayerStoreDataConsensusMapVisible() : LayerStoreData(FileTypeList({FileTypes::CONSENSUSXML}))
    {
    }

    // docu in base class
    void saveToFile(const String& filename, const ProgressLogger::LogType lt) const override;

    void storeVisibleCM(const ConsensusMap& cm, const RangeAllType& visible_range, const DataFilters& layer_filters);

  private:
    ConsensusMap cm_; 
  };

  class OPENMS_GUI_DLLAPI LayerStoreDataConsensusMapAll : public LayerStoreData
  {
  public:
    LayerStoreDataConsensusMapAll() : LayerStoreData(FileTypeList({FileTypes::CONSENSUSXML}))
    {
    }

    // docu in base class
    void saveToFile(const String& filename, const ProgressLogger::LogType lt) const override;

    void storeFullCM(const ConsensusMap& cm);

  private:
    const ConsensusMap* full_cm_ = nullptr; 
  };



  class OPENMS_GUI_DLLAPI LayerStoreDataIdentVisible : public LayerStoreData
  {
  public:
    LayerStoreDataIdentVisible() : LayerStoreData(FileTypeList({FileTypes::IDXML}))
    {
    }

    // docu in base class
    void saveToFile(const String& filename, const ProgressLogger::LogType lt) const override;

    void storeVisibleIdent(const IPeptideIds::PepIds& ids, const RangeAllType& visible_range, const DataFilters& layer_filters);

  private:
    IPeptideIds::PepIds ids_; 
  };

  class OPENMS_GUI_DLLAPI LayerStoreDataIdentAll : public LayerStoreData
  {
  public:
    LayerStoreDataIdentAll() : LayerStoreData(FileTypeList({FileTypes::IDXML}))
    {
    }

    // docu in base class
    void saveToFile(const String& filename, const ProgressLogger::LogType lt) const override;

    void storeFullIdent(const IPeptideIds::PepIds& ids);

  private:
    const IPeptideIds::PepIds* full_ids_ = nullptr; 
  };

} // namespace OpenMS