LayerData.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// 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
 
// OpenMS_GUI config
#include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
 
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/OnDiscMSExperiment.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/VISUAL/LogWindow.h>
#include <OpenMS/VISUAL/MultiGradient.h>
#include <OpenMS/VISUAL/ANNOTATION/Annotations1DContainer.h>
#include <OpenMS/FILTERING/DATAREDUCTION/DataFilters.h>
 
#include <boost/shared_ptr.hpp>
 
#include <vector>
#include <bitset>
 
namespace OpenMS
{
 
  class OPENMS_GUI_DLLAPI LayerData
  {
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;
 
 
    LayerData() :
      flags(),
      visible(true),
      flipped(false),
      type(DT_UNKNOWN),
      name_(),
      filename(),
      peptides(),
      param(),
      gradient(),
      filters(),
      annotations_1d(),
      peak_colors_1d(),
      modifiable(false),
      modified(false),
      label(L_NONE),
      peptide_id_index(-1),
      peptide_hit_index(-1),
      features(new FeatureMapType()),
      consensus(new ConsensusMapType()),
      peaks(new ExperimentType()),
      on_disc_peaks(new OnDiscMSExperiment()),
      chromatograms(new ExperimentType()),
      current_spectrum_(0),
      cached_spectrum_()
    {
      annotations_1d.resize(1);
    }
 
    LayerData(const LayerData& ld) = delete;
    LayerData& operator=(const LayerData& ld) = delete;
 
    LayerData(LayerData&& ld) = default;
 
    LayerData& operator=(LayerData&& ld) = default;
 
    const FeatureMapSharedPtrType & getFeatureMap() const
    {
      return features;
    }
 
    FeatureMapSharedPtrType & getFeatureMap()
    {
      return features;
    }
 
    const ConsensusMapSharedPtrType & getConsensusMap() const
    {
      return consensus;
    }
 
    ConsensusMapSharedPtrType & getConsensusMap()
    {
      return consensus;
    }
 
    const ConstExperimentSharedPtrType getPeakData() const;
 
    const ExperimentSharedPtrType & getPeakDataMuteable() {return peaks;}
 
    void setPeakData(ExperimentSharedPtrType p)
    {
      peaks = p;
      updateCache_();
    }
 
    void setOnDiscPeakData(ODExperimentSharedPtrType p)
    {
      on_disc_peaks = p;
    }
 
    const ODExperimentSharedPtrType & getOnDiscPeakData() const
    {
      return on_disc_peaks;
    }
 
    const ExperimentSharedPtrType & getChromatogramData() const
    {
      return chromatograms;
    }
 
    ExperimentSharedPtrType & getChromatogramData()
    {
      return chromatograms;
    }
 
    bool annotate(const std::vector<PeptideIdentification>& identifications,
                  const std::vector<ProteinIdentification>& protein_identifications);
 
 
    const Annotations1DContainer & getCurrentAnnotations() const
    {
      return annotations_1d[current_spectrum_];
    }
 
    Annotations1DContainer & getCurrentAnnotations()
    {
      return annotations_1d[current_spectrum_];
    }
 
    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
    {
      if (spectrum_idx == current_spectrum_) return cached_spectrum_;
 
      if ((*peaks)[spectrum_idx].size() > 0)
      {
        return (*peaks)[spectrum_idx];
      }
      else if (!on_disc_peaks->empty())
      {
        return on_disc_peaks->getSpectrum(spectrum_idx);
      }
      return (*peaks)[spectrum_idx];
    }
      
    Size getCurrentSpectrumIndex() const
    {
      return current_spectrum_;
    }
 
    void setCurrentSpectrumIndex(Size index)
    {
      current_spectrum_ = index;
      updateCache_();
    }
 
    bool isIonMobilityData() const
    {
      return this->getPeakData()->size() > 0 &&
             this->getPeakData()->metaValueExists("is_ion_mobility") &&
             this->getPeakData()->getMetaValue("is_ion_mobility").toBool();
    }
 
    void labelAsIonMobilityData() const
    {
      peaks->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()
    {
      peaks->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()
    {
      peaks->setMetaValue("is_chromatogram", "true");
    }
 
    void remove_chromatogram_flag()
    {
      if (this->chromatogram_flag_set())
      {
        peaks->removeMetaValue("is_chromatogram");
      }
    }
    
    void updateRanges();
 
    float getMinIntensity() const;
 
    float getMaxIntensity() const;
 
    void synchronizePeakAnnotations();
 
    void removePeakAnnotationsFromPeptideHit(const std::vector<Annotation1DItem*>& selected_annotations);
 
    bool visible;
 
    bool flipped;
 
    DataType type;
 
    private:
    String name_;
 
    public:
      const String& getName() const
      {
        return name_;
      }
      void setName(const String& new_name)
      {
        name_ = new_name;
      }
 
    String filename;
 
    std::vector<PeptideIdentification> peptides;
 
    Param param;
 
    MultiGradient gradient;
 
    DataFilters filters;
 
    std::vector<Annotations1DContainer> annotations_1d;
 
    std::vector<QColor> peak_colors_1d;
 
    bool modifiable;
 
    bool modified;
 
    LabelType label;
 
    int peptide_id_index;
    int peptide_hit_index;
 
    String getDecoratedName() const;
 
private:
    void updateCache_();
 
    void updatePeptideHitAnnotations_(PeptideHit& hit);
 
    FeatureMapSharedPtrType features;
 
    ConsensusMapSharedPtrType consensus;
 
    ExperimentSharedPtrType peaks;
 
    ODExperimentSharedPtrType on_disc_peaks;
 
    ExperimentSharedPtrType chromatograms;
 
    Size current_spectrum_;
 
    ExperimentType::SpectrumType cached_spectrum_;
  };
 
  class LayerAnnotatorBase
  {
    public:
      LayerAnnotatorBase(const FileTypes::FileTypeList& supported_types, const String& file_dialog_text);
      
      bool annotate(LayerData& layer, LogWindow& log, const String& current_path) const;
 
    protected:
      virtual bool annotateWorker_(LayerData& layer, const String& filename, LogWindow& log) const = 0;
      
      const FileTypes::FileTypeList supported_types_;
      const String file_dialog_text_;
  };
 
  class LayerAnnotatorPeptideID
    : public LayerAnnotatorBase
  {
    public:
      LayerAnnotatorPeptideID()
       : LayerAnnotatorBase(std::vector<FileTypes::Type>{ FileTypes::IDXML, FileTypes::MZIDENTML },
                            "Select peptide identification data")
      {}
 
  protected:
    virtual bool annotateWorker_(LayerData& layer, const String& filename, LogWindow& log) const;
  };
 
  class LayerAnnotatorAMS
    : public LayerAnnotatorBase
  {
  public:
    LayerAnnotatorAMS()
      : LayerAnnotatorBase(std::vector<FileTypes::Type>{ FileTypes::FEATUREXML },
                           "Select AccurateMassSearch's featureXML file")
    {}
 
  protected:
    virtual bool annotateWorker_(LayerData& layer, const String& filename, LogWindow& log) const;
  };
 
  OPENMS_GUI_DLLAPI std::ostream& operator<<(std::ostream & os, const LayerData & rhs);
 
} //namespace