LayerDataBase.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// 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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// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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//
// --------------------------------------------------------------------------
// $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/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/StandardTypes.h>

#include <OpenMS/FILTERING/DATAREDUCTION/DataFilters.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/OnDiscMSExperiment.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/VISUAL/ANNOTATION/Annotations1DContainer.h>
//#include <OpenMS/VISUAL/Painter1DBase.h>
#include <OpenMS/VISUAL/LogWindow.h>
#include <OpenMS/VISUAL/MultiGradient.h>

#include <boost/shared_ptr.hpp>

#include <bitset>
#include <vector>

class QWidget;

namespace OpenMS
{
  class LayerStatistics;
  class OSWData;
  class Painter1DBase;

  class OPENMS_GUI_DLLAPI LayerDataBase
  {
  public:
    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
    };

    std::bitset<SIZE_OF_FLAGS> 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;


    LayerDataBase() = delete;
    LayerDataBase(const DataType type) : type(type) {};
    LayerDataBase(const LayerDataBase& ld) = delete;
    LayerDataBase& operator=(const LayerDataBase& ld) = delete;
    LayerDataBase(LayerDataBase&& ld) = default;
    LayerDataBase& operator=(LayerDataBase&& ld) = default;
    virtual ~LayerDataBase() = default;

    virtual std::unique_ptr<Painter1DBase> getPainter1D() const = 0;


    const FeatureMapSharedPtrType& getFeatureMap() const
    {
      return features_;
    }

    FeatureMapSharedPtrType& getFeatureMap()
    {
      return features_;
    }

    const ConsensusMapSharedPtrType& getConsensusMap() const
    {
      return consensus_map_;
    }

    ConsensusMapSharedPtrType& getConsensusMap()
    {
      return consensus_map_;
    }

    const ConstExperimentSharedPtrType getPeakData() const;

    const ExperimentSharedPtrType& getPeakDataMuteable()
    {
      return peak_map_;
    }

    void setPeakData(ExperimentSharedPtrType p)
    {
      peak_map_ = p;
      updateCache_();
    }

    void setOnDiscPeakData(ODExperimentSharedPtrType p)
    {
      on_disc_peaks = p;
    }

    const ODExperimentSharedPtrType& getOnDiscPeakData() const
    {
      return on_disc_peaks;
    }

    const ExperimentSharedPtrType& getChromatogramData() const
    {
      return chromatogram_map_;
    }

    ExperimentSharedPtrType& getChromatogramData()
    {
      return chromatogram_map_;
    }

    OSWDataSharedPtrType& getChromatogramAnnotation();

    const OSWDataSharedPtrType& getChromatogramAnnotation() const;

    void setChromatogramAnnotation(OSWData&& data);

    bool annotate(const std::vector<PeptideIdentification>& identifications,
                  const std::vector<ProteinIdentification>& protein_identifications);


    const Annotations1DContainer& getCurrentAnnotations() const
    {
      return annotations_1d[current_spectrum_idx_];
    }

    Annotations1DContainer& getCurrentAnnotations()
    {
      return annotations_1d[current_spectrum_idx_];
    }

    const Annotations1DContainer& getAnnotations(Size spectrum_index) const
    {
      return annotations_1d[spectrum_index];
    }

    Annotations1DContainer& getAnnotations(Size spectrum_index)
    {
      return annotations_1d[spectrum_index];
    }

    const ExperimentType::SpectrumType& getCurrentSpectrum() const;

    void sortCurrentSpectrumByPosition()
    {
      cached_spectrum_.sortByPosition();
    }

    const ExperimentType::SpectrumType getSpectrum(Size spectrum_idx) const;

    Size getCurrentSpectrumIndex() const
    {
      return current_spectrum_idx_;
    }

    void setCurrentSpectrumIndex(Size index)
    {
      current_spectrum_idx_ = index;
      updateCache_();
    }


    ExperimentSharedPtrType getFullChromData()
    {
      ExperimentSharedPtrType exp_sptr(getChromatogramData().get() == nullptr ||
                                               getChromatogramData().get()->getNrChromatograms() == 0 ?
                                           getPeakDataMuteable() :
                                           getChromatogramData());
      return exp_sptr;
    }

    bool isIonMobilityData() const
    {
      return this->getPeakData()->size() > 0 &&
             this->getPeakData()->metaValueExists("is_ion_mobility") &&
             this->getPeakData()->getMetaValue("is_ion_mobility").toBool();
    }

    void labelAsIonMobilityData() const
    {
      peak_map_->setMetaValue("is_ion_mobility", "true");
    }

    bool isDIAData() const
    {
      return this->getPeakData()->size() > 0 &&
             this->getPeakData()->metaValueExists("is_dia_data") &&
             this->getPeakData()->getMetaValue("is_dia_data").toBool();
    }

    void labelAsDIAData()
    {
      peak_map_->setMetaValue("is_dia_data", "true");
    }

    bool chromatogram_flag_set() const
    {
      return this->getPeakData()->size() > 0 &&
             this->getPeakData()->metaValueExists("is_chromatogram") &&
             this->getPeakData()->getMetaValue("is_chromatogram").toBool();
    }

    void set_chromatogram_flag()
    {
      peak_map_->setMetaValue("is_chromatogram", "true");
    }

    void remove_chromatogram_flag()
    {
      if (this->chromatogram_flag_set())
      {
        peak_map_->removeMetaValue("is_chromatogram");
      }
    }

    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;

    void synchronizePeakAnnotations();

    void removePeakAnnotationsFromPeptideHit(const std::vector<Annotation1DItem*>& selected_annotations);

    bool visible = true;

    bool flipped = false;

    DataType type = DT_UNKNOWN;

  private:
    String name_;

  public:
    const String& getName() const
    {
      return name_;
    }
    void setName(const String& new_name)
    {
      name_ = new_name;
    }

    String filename;

    Param param;

    MultiGradient gradient;

    DataFilters filters;

    std::vector<Annotations1DContainer> annotations_1d = std::vector<Annotations1DContainer>(1);

    std::vector<QColor> peak_colors_1d;

    bool modifiable = false;

    bool modified = false;

    LabelType label = L_NONE;

    int peptide_id_index = -1;
    int peptide_hit_index = -1;

    String getDecoratedName() const;

  protected:
    void updateCache_();

    void updatePeptideHitAnnotations_(PeptideHit& hit);

    FeatureMapSharedPtrType features_ = FeatureMapSharedPtrType(new FeatureMapType());

    ConsensusMapSharedPtrType consensus_map_ = ConsensusMapSharedPtrType(new ConsensusMapType());

    ExperimentSharedPtrType peak_map_ = ExperimentSharedPtrType(new ExperimentType());

    ODExperimentSharedPtrType on_disc_peaks = ODExperimentSharedPtrType(new OnDiscMSExperiment());

    ExperimentSharedPtrType chromatogram_map_ = ExperimentSharedPtrType(new ExperimentType());

    OSWDataSharedPtrType chrom_annotation_;

    Size current_spectrum_idx_ = 0;

    ExperimentType::SpectrumType cached_spectrum_;
  };

  class LayerAnnotatorBase
  {
  public:
    LayerAnnotatorBase(const FileTypeList& supported_types, const String& file_dialog_text, QWidget* gui_lock);

    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