LayerDataBase.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   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;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// 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: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/Param.h>
#include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
 
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/FILTERING/DATAREDUCTION/DataFilters.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/OnDiscMSExperiment.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/VISUAL/LogWindow.h>
#include <OpenMS/VISUAL/MISC/CommonDefs.h>
#include <OpenMS/VISUAL/MultiGradient.h>
#include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
 
#include <boost/shared_ptr.hpp>
 
#include <bitset>
#include <vector>
 
class QWidget;
 
namespace OpenMS
{
  class LayerData1DBase;
  class LayerStoreData;
  class LayerStatistics;
  class OSWData;
  class Painter1DBase;
  class Painter2DBase;
 
  template <int N_DIM> class DimMapper;
 
  struct LayerDataDefs
  {
 
    struct ProjectionData
    {
      ProjectionData();
      ProjectionData(ProjectionData&&);
      ~ProjectionData(); // needs to be implemented in cpp, since inline would require a full definition of LayerData1DBase;
 
      std::unique_ptr<LayerData1DBase> projection_ontoX;
      std::unique_ptr<LayerData1DBase> projection_ontoY;
      struct Summary {
        UInt number_of_datapoints {0};
        Peak1D::IntensityType max_intensity {0};
        double sum_intensity {0}; // double since sum could get large
      } stats;
    };
 
    enum DataType
    {
      DT_PEAK,         
      DT_CHROMATOGRAM, 
      DT_FEATURE,      
      DT_CONSENSUS,    
      DT_IDENT,        
      DT_UNKNOWN       
    };
 
    enum Flags
    {
      F_HULL,        
      F_HULLS,       
      F_UNASSIGNED,  
      P_PRECURSORS,  
      P_PROJECTIONS, 
      C_ELEMENTS,    
      I_PEPTIDEMZ,   
      I_LABELS,      
      SIZE_OF_FLAGS
    };
 
    enum LabelType
    {
      L_NONE,       
      L_INDEX,      
      L_META_LABEL, 
      L_ID,         
      L_ID_ALL,     
      SIZE_OF_LABEL_TYPE
    };
 
    static const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE];
 
    typedef FeatureMap FeatureMapType;
 
    typedef boost::shared_ptr<FeatureMap> FeatureMapSharedPtrType;
 
    typedef ConsensusMap ConsensusMapType;
 
    typedef boost::shared_ptr<ConsensusMap> ConsensusMapSharedPtrType;
 
    typedef PeakMap ExperimentType;
 
    typedef boost::shared_ptr<ExperimentType> ExperimentSharedPtrType;
 
    typedef boost::shared_ptr<const ExperimentType> ConstExperimentSharedPtrType;
 
    typedef boost::shared_ptr<OnDiscMSExperiment> ODExperimentSharedPtrType;
 
    typedef boost::shared_ptr<OSWData> OSWDataSharedPtrType;
  };
 
#ifdef _MSC_VER
  #pragma warning(disable : 4250) // 'class1' : inherits 'class2::member' via dominance
#endif
  class OPENMS_GUI_DLLAPI LayerDataBase : public LayerDataDefs
  {
  public:
    std::bitset<SIZE_OF_FLAGS> flags;
 
 
    LayerDataBase() = delete;     // <-- this is the problem. Call assignment op in 1DPeak???
    explicit LayerDataBase(const DataType type) : type(type) {}
    LayerDataBase(const LayerDataBase& ld) = default;
    LayerDataBase& operator=(const LayerDataBase& ld) = delete;
    LayerDataBase(LayerDataBase&& ld) = delete;
    LayerDataBase& operator=(LayerDataBase&& ld) = delete;
    virtual ~LayerDataBase() = default;
 
    virtual std::unique_ptr<Painter2DBase> getPainter2D() const = 0;
 
 
    virtual std::unique_ptr <LayerData1DBase> to1DLayer() const = 0;
 
    virtual std::unique_ptr<LayerStoreData> storeVisibleData(const RangeAllType& /*visible_range*/, const DataFilters& /*layer_filters*/) const
    {
      throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
    virtual std::unique_ptr<LayerStoreData> storeFullData() const
    {
      throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
 
    // todo: put this into a LayerData2DBase class, since a LayerData1DPeak should not implement this.
    virtual ProjectionData getProjection(const DIM_UNIT unit_x, const DIM_UNIT unit_y, const RangeAllType& area) const = 0;
 
    virtual PeakIndex findClosestDataPoint(const RangeAllType& /*area*/) const
    {
      throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
 
    virtual PeakIndex findHighestDataPoint(const RangeAllType& /*area*/) const
    {
      throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
 
 
    virtual PointXYType peakIndexToXY(const PeakIndex& peak, const DimMapper<2>& mapper) const = 0;
 
    virtual String getDataArrayDescription(const PeakIndex& /*peak_index*/)
    {
      throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }
 
    virtual bool annotate(const std::vector<PeptideIdentification>& identifications,
                          const std::vector<ProteinIdentification>& protein_identifications);
 
 
    virtual void updateRanges() = 0;
 
    float getMinIntensity() const;
 
    float getMaxIntensity() const;
 
    using RangeAllType = RangeManager<RangeRT, RangeMZ, RangeIntensity, RangeMobility>;
 
    virtual RangeAllType getRange() const = 0;
 
    virtual std::unique_ptr<LayerStatistics> getStats() const = 0;
 
    const String& getName() const
    {
      return name_;
    }
    void setName(const String& new_name)
    {
      name_ = new_name;
    }
 
    const String& getNameSuffix() const
    {
      return name_suffix_;
    }
    void setNameSuffix(const String& decorator)
    {
      name_suffix_ = decorator;
    }
 
    virtual String getDecoratedName() const;
 
    bool visible = true;
 
    DataType type = DT_UNKNOWN;
 
    String filename;
 
    Param param;
 
    MultiGradient gradient;
 
    DataFilters filters;
 
    bool modifiable = false;
 
    bool modified = false;
 
    LabelType label = L_NONE;
 
    int peptide_id_index = -1;
    int peptide_hit_index = -1;
 
  private:
    String name_;
    String name_suffix_;
  };
 
  class LayerAnnotatorBase
  {
  public:
    LayerAnnotatorBase(const FileTypeList& supported_types, const String& file_dialog_text, QWidget* gui_lock);
    
    virtual ~LayerAnnotatorBase() = default;
 
    bool annotateWithFileDialog(LayerDataBase& layer, LogWindow& log, const String& current_path) const;
 
    bool annotateWithFilename(LayerDataBase& layer, LogWindow& log, const String& filename) const;
 
    static std::unique_ptr<LayerAnnotatorBase> getAnnotatorWhichSupports(const FileTypes::Type& type);
 
    static std::unique_ptr<LayerAnnotatorBase> getAnnotatorWhichSupports(const String& filename);
 
  protected:
    virtual bool annotateWorker_(LayerDataBase& layer, const String& filename, LogWindow& log) const = 0;
 
    const FileTypeList supported_types_;
    const String file_dialog_text_;
    QWidget* gui_lock_ = nullptr;
  };
 
  class LayerAnnotatorPeptideID : public LayerAnnotatorBase
  {
  public:
    LayerAnnotatorPeptideID(QWidget* gui_lock) :
        LayerAnnotatorBase(std::vector<FileTypes::Type>{FileTypes::IDXML, FileTypes::MZIDENTML},
                           "Select peptide identification data", gui_lock)
    {
    }
 
  protected:
    virtual bool annotateWorker_(LayerDataBase& layer, const String& filename, LogWindow& log) const;
  };
 
  class LayerAnnotatorAMS : public LayerAnnotatorBase
  {
  public:
    LayerAnnotatorAMS(QWidget* gui_lock) :
        LayerAnnotatorBase(std::vector<FileTypes::Type>{FileTypes::FEATUREXML},
                           "Select AccurateMassSearch's featureXML file", gui_lock)
    {
    }
 
  protected:
    virtual bool annotateWorker_(LayerDataBase& layer, const String& filename, LogWindow& log) const;
  };
 
  class LayerAnnotatorOSW : public LayerAnnotatorBase
  {
  public:
    LayerAnnotatorOSW(QWidget* gui_lock) :
        LayerAnnotatorBase(std::vector<FileTypes::Type>{FileTypes::OSW},
                           "Select OpenSwath/pyProphet output file", gui_lock)
    {
    }
 
  protected:
    virtual bool annotateWorker_(LayerDataBase& layer, const String& filename, LogWindow& log) const;
  };
 
  OPENMS_GUI_DLLAPI std::ostream& operator<<(std::ostream& os, const LayerDataBase& rhs);
 
}// namespace OpenMS