OpenMS  3.0.0
TVIdentificationViewController.h
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31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Timo Sachsenberg $
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34 
35 #pragma once
36 
40 #include <vector>
41 
42 namespace OpenMS
43 {
44  class NASequence;
45  class SpectraIDViewTab;
46  class TOPPViewBase;
47 
52  : public TVControllerBase
53  {
54  Q_OBJECT
55 
56  public:
59 
60  public slots:
62  virtual void showSpectrumAsNew1D(int spectrum_index, int peptide_id_index, int peptide_hit_index);
63 
65  virtual void showSpectrumAsNew1D(int index);
66 
68  virtual void activate1DSpectrum(int spectrum_index, int peptide_id_index, int peptide_hit_index);
69 
71  virtual void activate1DSpectrum(int index);
72 
74  virtual void deactivate1DSpectrum(int index);
75 
77  void activateBehavior() override;
78 
80  void deactivateBehavior() override;
81 
82  void setVisibleArea1D(double l, double h);
83 
84  private:
86  void addPrecursorLabels1D_(const std::vector<Precursor>& pcs);
87 
89  void removeTemporaryAnnotations_(Size spectrum_index);
90 
93 
95  void addPeakAnnotationsFromID_(const PeptideHit& hit);
96 
99 
101  void removeGraphicalPeakAnnotations_(int spectrum_index);
102 
104  void addPeakAnnotations_(const std::vector<PeptideIdentification>& ph);
105 
107  String n_times(Size n, String input);
108 
110  void extractCoverageStrings(std::vector<PeptideHit::PeakAnnotation> frag_annotations, String& alpha_string, String& beta_string, Size alpha_size, Size beta_size);
111 
113  template <typename SeqType>
114  String generateSequenceDiagram_(const SeqType& seq, const std::vector<PeptideHit::PeakAnnotation>& annotations, const StringList& top_ions, const StringList& bottom_ions);
115 
117  void generateSequenceRow_(const AASequence& seq, std::vector<String>& row);
118 
120  void generateSequenceRow_(const NASequence& seq, std::vector<String>& row);
121 
123  String collapseStringVector(std::vector<String> strings);
124 
125  private:
129  std::vector<Annotation1DItem*> temporary_annotations_;
130  };
131 }
OpenMS::TVIdentificationViewController
Behavior of TOPPView in identification mode.
Definition: TVIdentificationViewController.h:51
OpenMS::TVIdentificationViewController::removeTemporaryAnnotations_
void removeTemporaryAnnotations_(Size spectrum_index)
Removes the precursor labels for from the specified 1D spectrum.
OpenMS::TVIdentificationViewController::addPeakAnnotationsFromID_
void addPeakAnnotationsFromID_(const PeptideHit &hit)
Add peak annotatios from id data structure.
OpenMS::TVIdentificationViewController::temporary_annotations_
std::vector< Annotation1DItem * > temporary_annotations_
Definition: TVIdentificationViewController.h:129
OpenMS::NASequence
Representation of a nucleic acid sequence.
Definition: NASequence.h:61
OpenMS::TVIdentificationViewController::generateSequenceRow_
void generateSequenceRow_(const AASequence &seq, std::vector< String > &row)
Helper function for generateSequenceDiagram_() - overload for peptides.
OpenMS::TVIdentificationViewController::generateSequenceDiagram_
String generateSequenceDiagram_(const SeqType &seq, const std::vector< PeptideHit::PeakAnnotation > &annotations, const StringList &top_ions, const StringList &bottom_ions)
Generates HTML for showing the sequence with annotations of matched fragments.
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::TOPPViewBase
Main window of TOPPView tool.
Definition: TOPPViewBase.h:126
OpenMS::TVIdentificationViewController::addTheoreticalSpectrumLayer_
void addTheoreticalSpectrumLayer_(const PeptideHit &ph)
Adds a theoretical spectrum as set from the preferences dialog for the peptide hit.
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::TVIdentificationViewController::activate1DSpectrum
virtual void activate1DSpectrum(int spectrum_index, int peptide_id_index, int peptide_hit_index)
Behavior for activate1DSpectrum.
OpenMS::TVIdentificationViewController::showSpectrumAsNew1D
virtual void showSpectrumAsNew1D(int spectrum_index, int peptide_id_index, int peptide_hit_index)
Behavior for showSpectrumAsNew1D.
SpectrumSettings.h
OpenMS::SpectraIDViewTab
Tabular visualization / selection of identified spectra.
Definition: SpectraIDViewTab.h:59
OpenMS::TVIdentificationViewController::removeGraphicalPeakAnnotations_
void removeGraphicalPeakAnnotations_(int spectrum_index)
remove all graphical peak annotations
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::TVControllerBase
Base behavior for different visualizaton modules in TOPPView.
Definition: TVControllerBase.h:47
OpenMS::TVIdentificationViewController::collapseStringVector
String collapseStringVector(std::vector< String > strings)
Helper function, that collapses a vector of Strings into one String.
LayerDataBase.h
OpenMS::TVIdentificationViewController::deactivate1DSpectrum
virtual void deactivate1DSpectrum(int index)
Behavior for deactivate1DSpectrum.
OpenMS::TVIdentificationViewController::removeTheoreticalSpectrumLayer_
void removeTheoreticalSpectrumLayer_()
removes all layer with theoretical spectrum generated in identification view
OpenMS::TVIdentificationViewController::setVisibleArea1D
void setVisibleArea1D(double l, double h)
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::Constants::h
const double h
Definition: Constants.h:162
TVControllerBase.h
OpenMS::TVIdentificationViewController::addPrecursorLabels1D_
void addPrecursorLabels1D_(const std::vector< Precursor > &pcs)
Adds labels for the provided precursors to the 1D spectrum.
OpenMS::TVIdentificationViewController::spec_id_view_
SpectraIDViewTab * spec_id_view_
Definition: TVIdentificationViewController.h:126
OpenMS::TVIdentificationViewController::deactivateBehavior
void deactivateBehavior() override
Slot for behavior deactivation.
OpenMS::TVIdentificationViewController::n_times
String n_times(Size n, String input)
Helper function for text formatting.
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::TVIdentificationViewController::addPeakAnnotations_
void addPeakAnnotations_(const std::vector< PeptideIdentification > &ph)
Adds annotation (compound name, adducts, ppm error) to a peak in 1D spectra.
OpenMS::TVIdentificationViewController::activateBehavior
void activateBehavior() override
Slot for behavior activation.
OpenMS::TVIdentificationViewController::TVIdentificationViewController
TVIdentificationViewController(TOPPViewBase *parent, SpectraIDViewTab *spec_id_view_)
Construct the behaviour with its parent.
OpenMS::TVIdentificationViewController::extractCoverageStrings
void extractCoverageStrings(std::vector< PeptideHit::PeakAnnotation > frag_annotations, String &alpha_string, String &beta_string, Size alpha_size, Size beta_size)
Helper function that turns fragment annotations into coverage Strings for visualization with the sequ...
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55