| OpenMS 2.5.0

TOPPViewIdentificationViewBehavior.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Timo Sachsenberg $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CHEMISTRY/NASequence.h>
38 #include <OpenMS/METADATA/SpectrumSettings.h>
39 #include <OpenMS/VISUAL/LayerData.h>
40 #include <vector>
41
42 namespace OpenMS
43 {
44 class TOPPViewBase;
45
49 class TOPPViewIdentificationViewBehavior
50 : public QObject
51 {
52 Q_OBJECT
54
55 //Feature map type
56 typedef LayerData::FeatureMapType FeatureMapType;
57 //Feature map managed type
58 typedef LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType;
59
60 //Consensus feature map type
61 typedef LayerData::ConsensusMapType ConsensusMapType;
62 //Consensus map managed type
63 typedef LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType;
64
65 //Peak map type
66 typedef LayerData::ExperimentType ExperimentType;
67 //Main managed data type (experiment)
68 typedef LayerData::ExperimentSharedPtrType ExperimentSharedPtrType;
70 typedef ExperimentType::SpectrumType SpectrumType;
72
73 public:
75 TOPPViewIdentificationViewBehavior(TOPPViewBase* parent);
76
77 public slots:
79 virtual void showSpectrumAs1D(int spectrum_index, int peptide_id_index, int peptide_hit_index);
80
82 virtual void showSpectrumAs1D(int index);
83
85 virtual void activate1DSpectrum(int spectrum_index, int peptide_id_index, int peptide_hit_index);
86
88 virtual void activate1DSpectrum(int index);
89
91 virtual void deactivate1DSpectrum(int index);
92
94 virtual void activateBehavior();
95
97 virtual void deactivateBehavior();
98
99 void setVisibleArea1D(double l, double h);
100
101 private:
103 void addPrecursorLabels1D_(const std::vector<Precursor>& pcs);
104
106 void removeTemporaryAnnotations_(Size spectrum_index);
107
109 void addTheoreticalSpectrumLayer_(const PeptideHit& ph);
110
112 void addPeakAnnotationsFromID_(const PeptideHit& hit);
113
115 void removeTheoreticalSpectrumLayer_();
116
118 void removeGraphicalPeakAnnotations_(int spectrum_index);
119
121 void addPeakAnnotations_(const std::vector<PeptideIdentification>& ph);
122
124 String n_times(Size n, String input);
125
127 void extractCoverageStrings(std::vector<PeptideHit::PeakAnnotation> frag_annotations, String& alpha_string, String& beta_string, Size alpha_size, Size beta_size);
128
130 template <typename SeqType>
131 String generateSequenceDiagram_(const SeqType& seq, const std::vector<PeptideHit::PeakAnnotation>& annotations, const StringList& top_ions, const StringList& bottom_ions);
132
134 void generateSequenceRow_(const AASequence& seq, std::vector<String>& row);
135
137 void generateSequenceRow_(const NASequence& seq, std::vector<String>& row);
138
140 String collapseStringVector(std::vector<String> strings);
141
142 private:
143 TOPPViewBase* tv_;
146 std::vector<Annotation1DItem*> temporary_annotations_;
147 };
148 }
OpenMS::TOPPViewIdentificationViewBehavior::setVisibleArea1D
void setVisibleArea1D(double l, double h)
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::TOPPViewIdentificationViewBehavior::addTheoreticalSpectrumLayer_
void addTheoreticalSpectrumLayer_(const PeptideHit &ph)
Adds a theoretical spectrum as set from the preferences dialog for the peptide hit.
OpenMS::TOPPViewIdentificationViewBehavior::generateSequenceRow_
void generateSequenceRow_(const AASequence &seq, std::vector< String > &row)
Helper function for generateSequenceDiagram_() - overload for peptides.
OpenMS::TOPPViewIdentificationViewBehavior::SpectrumType
ExperimentType::SpectrumType SpectrumType
Peak spectrum type.
Definition: TOPPViewIdentificationViewBehavior.h:70
OpenMS::TOPPViewIdentificationViewBehavior::TOPPViewIdentificationViewBehavior
TOPPViewIdentificationViewBehavior(TOPPViewBase *parent)
Construct the behaviour with its parent.
OpenMS::TOPPViewBase
Main window of TOPPView tool.
Definition: TOPPViewBase.h:124
OpenMS::TOPPViewIdentificationViewBehavior::tv_
TOPPViewBase * tv_
Definition: TOPPViewIdentificationViewBehavior.h:143
OpenMS::TOPPViewIdentificationViewBehavior
Behavior of TOPPView in identification mode.
Definition: TOPPViewIdentificationViewBehavior.h:49
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
LayerData.h
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
NASequence.h
OpenMS::TOPPViewIdentificationViewBehavior::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::TOPPViewIdentificationViewBehavior::ExperimentSharedPtrType
LayerData::ExperimentSharedPtrType ExperimentSharedPtrType
Definition: TOPPViewIdentificationViewBehavior.h:68
OpenMS::TOPPViewIdentificationViewBehavior::n_times
String n_times(Size n, String input)
Helper function for text formatting.
OpenMS::TOPPViewIdentificationViewBehavior::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::TOPPViewIdentificationViewBehavior::deactivateBehavior
virtual void deactivateBehavior()
Slot for behavior deactivation.
OpenMS::TOPPViewIdentificationViewBehavior::FeatureMapSharedPtrType
LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType
Definition: TOPPViewIdentificationViewBehavior.h:58
OpenMS::TOPPViewIdentificationViewBehavior::FeatureMapType
LayerData::FeatureMapType FeatureMapType
Definition: TOPPViewIdentificationViewBehavior.h:56
OpenMS::TOPPViewIdentificationViewBehavior::showSpectrumAs1D
virtual void showSpectrumAs1D(int spectrum_index, int peptide_id_index, int peptide_hit_index)
Behavior for showSpectrumAs1D.
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::TOPPViewIdentificationViewBehavior::ConsensusMapType
LayerData::ConsensusMapType ConsensusMapType
Definition: TOPPViewIdentificationViewBehavior.h:61
OpenMS::LayerData::ExperimentSharedPtrType
boost::shared_ptr< ExperimentType > ExperimentSharedPtrType
SharedPtr on MSExperiment.
Definition: LayerData.h:149
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54
OpenMS::TOPPViewIdentificationViewBehavior::ConsensusMapSharedPtrType
LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType
Definition: TOPPViewIdentificationViewBehavior.h:63
OpenMS::TOPPViewIdentificationViewBehavior::deactivate1DSpectrum
virtual void deactivate1DSpectrum(int index)
Behavior for deactivate1DSpectrum.
OpenMS::TOPPViewIdentificationViewBehavior::removeGraphicalPeakAnnotations_
void removeGraphicalPeakAnnotations_(int spectrum_index)
remove all graphical peak annotations
OpenMS::TOPPViewIdentificationViewBehavior::removeTemporaryAnnotations_
void removeTemporaryAnnotations_(Size spectrum_index)
Removes the precursor labels for from the specified 1D spectrum.
OpenMS::TOPPViewIdentificationViewBehavior::collapseStringVector
String collapseStringVector(std::vector< String > strings)
Helper function, that collapses a vector of Strings into one String.
SpectrumSettings.h
OpenMS::LayerData::ConsensusMapSharedPtrType
boost::shared_ptr< ConsensusMap > ConsensusMapSharedPtrType
SharedPtr on consensus features.
Definition: LayerData.h:143
OpenMS::NASequence
Representation of a nucleic acid sequence.
Definition: NASequence.h:62
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::TOPPViewIdentificationViewBehavior::ExperimentType
LayerData::ExperimentType ExperimentType
Definition: TOPPViewIdentificationViewBehavior.h:66
OpenMS::TOPPViewIdentificationViewBehavior::temporary_annotations_
std::vector< Annotation1DItem * > temporary_annotations_
Definition: TOPPViewIdentificationViewBehavior.h:146
OpenMS::LayerData::FeatureMapSharedPtrType
boost::shared_ptr< FeatureMap > FeatureMapSharedPtrType
SharedPtr on feature map.
Definition: LayerData.h:137
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::TOPPViewIdentificationViewBehavior::removeTheoreticalSpectrumLayer_
void removeTheoreticalSpectrumLayer_()
removes all layer with theoretical spectrum generated in identification view
OpenMS::TOPPViewIdentificationViewBehavior::addPeakAnnotations_
void addPeakAnnotations_(const std::vector< PeptideIdentification > &ph)
Adds annotation (compound name, adducts, ppm error) to a peak in 1D spectra.
OpenMS::TOPPViewIdentificationViewBehavior::addPeakAnnotationsFromID_
void addPeakAnnotationsFromID_(const PeptideHit &hit)
Add peak annotatios from id data structure.
OpenMS::TOPPViewIdentificationViewBehavior::addPrecursorLabels1D_
void addPrecursorLabels1D_(const std::vector< Precursor > &pcs)
Adds labels for the provided precursors to the 1D spectrum.
OpenMS::TOPPViewIdentificationViewBehavior::activate1DSpectrum
virtual void activate1DSpectrum(int spectrum_index, int peptide_id_index, int peptide_hit_index)
Behavior for activate1DSpectrum.
OpenMS::TOPPViewIdentificationViewBehavior::activateBehavior
virtual void activateBehavior()
Slot for behavior activation.
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
QObject
OpenMS::Constants::h
const double h