text: // --------------------------------------------------------------------------
  //                   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: Timo Sachsenberg $
  // --------------------------------------------------------------------------
  
  #pragma once
  
  #include <OpenMS/METADATA/SpectrumSettings.h>
  #include <OpenMS/VISUAL/LayerData.h>
  #include <OpenMS/VISUAL/TVControllerBase.h>
  #include <vector>
  
  namespace OpenMS
  {
    class NASequence;
    class SpectraIDViewTab;
    class TOPPViewBase;
  
    /**
    @brief Behavior of TOPPView in identification mode.
    */
    class TVIdentificationViewController
      : public TVControllerBase
    {
      Q_OBJECT
  
    public:
      /// Construct the behaviour with its parent
      TVIdentificationViewController(TOPPViewBase* parent, SpectraIDViewTab* spec_id_view_);
  
    public slots:
      /// Behavior for showSpectrumAs1D
      virtual void showSpectrumAs1D(int spectrum_index, int peptide_id_index, int peptide_hit_index);
  
      /// Show spectrum without selecting an identification
      virtual void showSpectrumAs1D(int index);
  
      /// Behavior for activate1DSpectrum
      virtual void activate1DSpectrum(int spectrum_index, int peptide_id_index, int peptide_hit_index);
  
      /// select spectrum without selecting an identification
      virtual void activate1DSpectrum(int index);
  
      /// Behavior for deactivate1DSpectrum
      virtual void deactivate1DSpectrum(int index);
  
      /// Slot for behavior activation
      void activateBehavior() override;
  
      /// Slot for behavior deactivation
      void deactivateBehavior() override;
  
      void setVisibleArea1D(double l, double h);
  
    private:
      /// Adds labels for the provided precursors to the 1D spectrum
      void addPrecursorLabels1D_(const std::vector<Precursor>& pcs);
  
      /// Removes the precursor labels for from the specified 1D spectrum
      void removeTemporaryAnnotations_(Size spectrum_index);
  
      /// Adds a theoretical spectrum as set from the preferences dialog for the peptide hit.
      void addTheoreticalSpectrumLayer_(const PeptideHit& ph);
  
      /// Add peak annotatios from id data structure
      void addPeakAnnotationsFromID_(const PeptideHit& hit);
  
      /// removes all layer with theoretical spectrum generated in identification view
      void removeTheoreticalSpectrumLayer_();
  
      /// remove all graphical peak annotations
      void removeGraphicalPeakAnnotations_(int spectrum_index);
  
      /// Adds annotation (compound name, adducts, ppm error) to a peak in 1D spectra
      void addPeakAnnotations_(const std::vector<PeptideIdentification>& ph);
  
      /// Helper function for text formatting
      String n_times(Size n, String input);
  
      /// Helper function that turns fragment annotations into coverage Strings for visualization with the sequence
      void extractCoverageStrings(std::vector<PeptideHit::PeakAnnotation> frag_annotations, String& alpha_string, String& beta_string, Size alpha_size, Size beta_size);
  
      /// Generates HTML for showing the sequence with annotations of matched fragments
      template <typename SeqType>
      String generateSequenceDiagram_(const SeqType& seq, const std::vector<PeptideHit::PeakAnnotation>& annotations, const StringList& top_ions, const StringList& bottom_ions);
  
      /// Helper function for generateSequenceDiagram_() - overload for peptides
      void generateSequenceRow_(const AASequence& seq, std::vector<String>& row);
  
      /// Helper function for generateSequenceDiagram_() - overload for oligonucleotides
      void generateSequenceRow_(const NASequence& seq, std::vector<String>& row);
  
      /// Helper function, that collapses a vector of Strings into one String
      String collapseStringVector(std::vector<String> strings);
  
    private:
      SpectraIDViewTab* spec_id_view_;
      /// Used to check which annotation handles have been added automatically by the identification view. Ownership
      /// of the AnnotationItems has the Annotation1DContainer
      std::vector<Annotation1DItem*> temporary_annotations_;
    };
  }
  