TVIdentificationViewController.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// 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.
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// 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
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// 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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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/METADATA/SpectrumSettings.h>
#include <OpenMS/VISUAL/LayerDataBase.h>
#include <OpenMS/VISUAL/TVControllerBase.h>
#include <vector>
 
namespace OpenMS
{
  class Annotation1DItem;
  class NASequence;
  class SpectraIDViewTab;
  class TOPPViewBase;
 
  class TVIdentificationViewController
    : public TVControllerBase
  {
    Q_OBJECT
 
  public:
    TVIdentificationViewController(TOPPViewBase* parent, SpectraIDViewTab* spec_id_view_);
 
  public slots:
    virtual void showSpectrumAsNew1D(int spectrum_index, int peptide_id_index, int peptide_hit_index);
 
    virtual void showSpectrumAsNew1D(int index);
 
    virtual void activate1DSpectrum(int spectrum_index, int peptide_id_index, int peptide_hit_index);
 
    virtual void activate1DSpectrum(int index);
 
    virtual void deactivate1DSpectrum(int index);
 
    void activateBehavior() override;
 
    void deactivateBehavior() override;
 
    void setVisibleArea1D(double l, double h);
 
  private:
    void addPrecursorLabels1D_(const std::vector<Precursor>& pcs);
 
    void removeTemporaryAnnotations_(Size spectrum_index);
 
    void addTheoreticalSpectrumLayer_(const PeptideHit& ph);
 
    void addPeakAnnotationsFromID_(const PeptideHit& hit);
 
    void removeTheoreticalSpectrumLayer_();
 
    void removeGraphicalPeakAnnotations_(int spectrum_index);
 
    void addPeakAnnotations_(const std::vector<PeptideIdentification>& ph);
 
    String n_times(Size n, const String& input);
 
    void extractCoverageStrings(std::vector<PeptideHit::PeakAnnotation> frag_annotations, String& alpha_string, String& beta_string, Size alpha_size, Size beta_size);
 
    template <typename SeqType>
    String generateSequenceDiagram_(const SeqType& seq, const std::vector<PeptideHit::PeakAnnotation>& annotations, const StringList& top_ions, const StringList& bottom_ions);
 
    void generateSequenceRow_(const AASequence& seq, std::vector<String>& row);
 
    void generateSequenceRow_(const NASequence& seq, std::vector<String>& row);
 
    String collapseStringVector(std::vector<String> strings);
 
  private:
    SpectraIDViewTab* spec_id_view_;
    std::vector<Annotation1DItem*> temporary_annotations_;
  };
}