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 2002-2023.
//
// 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
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// 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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// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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