TOPPViewIdentificationViewBehavior.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// 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
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// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------

#pragma once

// #include <OpenMS/CHEMISTRY/NASequence.h>
#include <OpenMS/METADATA/SpectrumSettings.h>
#include <OpenMS/VISUAL/LayerData.h>
#include <vector>

namespace OpenMS
{
  class TOPPViewBase;

  class TOPPViewIdentificationViewBehavior
    : public QObject
  {
    Q_OBJECT

    //Feature map type
    typedef LayerData::FeatureMapType FeatureMapType;
    //Feature map managed type
    typedef LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType;

    //Consensus feature map type
    typedef LayerData::ConsensusMapType ConsensusMapType;
    //Consensus  map managed type
    typedef LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType;

    //Peak map type
    typedef LayerData::ExperimentType ExperimentType;
    //Main managed data type (experiment)
    typedef LayerData::ExperimentSharedPtrType ExperimentSharedPtrType;
    typedef ExperimentType::SpectrumType SpectrumType;

  public:
    TOPPViewIdentificationViewBehavior(TOPPViewBase* parent);

  public slots:
    virtual void showSpectrumAs1D(int spectrum_index, int peptide_id_index, int peptide_hit_index);

    virtual void showSpectrumAs1D(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);

    virtual void activateBehavior();

    virtual void deactivateBehavior();

    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, 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:
    TOPPViewBase* tv_;
    std::vector<Annotation1DItem*> temporary_annotations_;
  };
}