LayerDataPeak.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/VISUAL/LayerDataBase.h>
#include <OpenMS/VISUAL/LayerData1DBase.h>
 
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
 
#include <vector>
 
namespace OpenMS
{
  class Annotation1DItem;
 
  class OPENMS_GUI_DLLAPI LayerDataPeak : public virtual LayerDataBase
  {
  public:
 
    using SpectrumType = ExperimentType::SpectrumType;
    using PeakType = SpectrumType::PeakType;
 
    LayerDataPeak();
    LayerDataPeak(const LayerDataPeak& ld) = default;
    LayerDataPeak& operator=(const LayerDataPeak& ld) = delete;
 
    std::unique_ptr<Painter2DBase> getPainter2D() const override;
 
    std::unique_ptr<LayerData1DBase> to1DLayer() const override;
 
    std::unique_ptr<LayerStoreData> storeVisibleData(const RangeAllType& visible_range, const DataFilters& layer_filters) const override;
 
    std::unique_ptr<LayerStoreData> storeFullData() const override;
 
    ProjectionData getProjection(const DIM_UNIT unit_x, const DIM_UNIT unit_y, const RangeAllType& area) const override;
 
    PeakIndex findHighestDataPoint(const RangeAllType& area) const override;
 
    void updateRanges() override
    {
      peak_map_->getMSExperiment().updateRanges();
      // on_disc_peaks_->updateRanges(); // note: this is not going to work since its on disk! We currently don't have a good way to access these ranges
    }
 
    RangeAllType getRange() const override
    {
      RangeAllType r;
      r.assign(peak_map_->getMSExperiment().spectrumRanges());
      return r;
    }
 
    PointXYType peakIndexToXY(const PeakIndex& peak, const DimMapper<2>& mapper) const override;
 
    String getDataArrayDescription(const PeakIndex& peak_index) override;
 
    std::unique_ptr<LayerStatistics> getStats() const override;
 
    bool annotate(const PeptideIdentificationList& identifications, const std::vector<ProteinIdentification>& protein_identifications) override;
 
    const ExperimentType::SpectrumType& getSpectrum(Size spectrum_idx) const
    {
      if (peak_map_->getMSExperiment()[spectrum_idx].size() > 0)
      {
        return peak_map_->getMSExperiment()[spectrum_idx];
      }
      if (!on_disc_peaks_->empty())
      {
        static MSSpectrum local_spec;
        local_spec = on_disc_peaks_->getSpectrum(spectrum_idx);
        return local_spec;
      }
      return peak_map_->getMSExperiment()[spectrum_idx];
    }
 
    const ConstExperimentSharedPtrType getPeakData() const;
 
    const ExperimentSharedPtrType& getPeakDataMuteable()
    {
      return peak_map_;
    }
 
    void setPeakData(ExperimentSharedPtrType p)
    {
      peak_map_ = p;
    }
 
    void setOnDiscPeakData(ODExperimentSharedPtrType p)
    {
      on_disc_peaks_ = p;
    }
 
    const ODExperimentSharedPtrType& getOnDiscPeakData() const
    {
      return on_disc_peaks_;
    }
 
 
    
    bool isIonMobilityData() const
    {
      const MSExperiment& exp = this->getPeakData()->getMSExperiment();
      return exp.size() > 0 
        && exp.metaValueExists("is_ion_mobility") 
        && exp.getMetaValue("is_ion_mobility").toBool();
    }
 
    void labelAsIonMobilityData() const
    {
      peak_map_->getMSExperiment().setMetaValue("is_ion_mobility", "true");
    }
 
    bool isDIAData() const
    {
      const MSExperiment& exp = this->getPeakData()->getMSExperiment();
      return exp.size() > 0 
        && exp.metaValueExists("is_dia_data") 
        && exp.getMetaValue("is_dia_data").toBool();
    }
 
    void labelAsDIAData()
    {
      peak_map_->getMSExperiment().setMetaValue("is_dia_data", "true");
    }
 
    bool chromatogram_flag_set() const
    {
      const MSExperiment& exp = this->getPeakData()->getMSExperiment();
      return exp.size() > 0 
        && exp.metaValueExists("is_chromatogram") 
        && exp.getMetaValue("is_chromatogram").toBool();
    }
 
    void set_chromatogram_flag()
    {
      peak_map_->getMSExperiment().setMetaValue("is_chromatogram", "true");
    }
 
    void remove_chromatogram_flag()
    {
      if (this->chromatogram_flag_set())
      {
        peak_map_->getMSExperiment().removeMetaValue("is_chromatogram");
      }
    }
 
 
  protected:
    ExperimentSharedPtrType peak_map_ = ExperimentSharedPtrType(new ExperimentType());
 
    ODExperimentSharedPtrType on_disc_peaks_ = ODExperimentSharedPtrType(new OnDiscMSExperiment());
  };
 
}// namespace OpenMS