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typedef LayerData::FeatureMapType | FeatureMapType |
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typedef LayerData::FeatureMapSharedPtrType | FeatureMapSharedPtrType |
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typedef LayerData::ConsensusMapType | ConsensusMapType |
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typedef LayerData::ConsensusMapSharedPtrType | ConsensusMapSharedPtrType |
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typedef LayerData::ExperimentType | ExperimentType |
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typedef LayerData::ExperimentSharedPtrType | ExperimentSharedPtrType |
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typedef ExperimentType::SpectrumType | SpectrumType |
| Peak spectrum type. More...
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TOPPViewBase * | tv_ |
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std::vector< Annotation1DItem * > | temporary_annotations_ |
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| TOPPViewIdentificationViewBehavior (TOPPViewBase *parent) |
| Construct the behaviour with its parent. More...
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virtual void | showSpectrumAs1D (int spectrum_index, int peptide_id_index, int peptide_hit_index) |
| Behavior for showSpectrumAs1D. More...
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virtual void | showSpectrumAs1D (int index) |
| Show spectrum without selecting an identification. More...
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virtual void | activate1DSpectrum (int spectrum_index, int peptide_id_index, int peptide_hit_index) |
| Behavior for activate1DSpectrum. More...
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virtual void | activate1DSpectrum (int index) |
| select spectrum without selecting an identification More...
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virtual void | deactivate1DSpectrum (int index) |
| Behavior for deactivate1DSpectrum. More...
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virtual void | activateBehavior () |
| Slot for behavior activation. More...
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virtual void | deactivateBehavior () |
| Slot for behavior deactivation. More...
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void | setVisibleArea1D (double l, double h) |
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void | addPrecursorLabels1D_ (const std::vector< Precursor > &pcs) |
| Adds labels for the provided precursors to the 1D spectrum. More...
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void | removeTemporaryAnnotations_ (Size spectrum_index) |
| Removes the precursor labels for from the specified 1D spectrum. More...
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void | addTheoreticalSpectrumLayer_ (const PeptideHit &ph) |
| Adds a theoretical spectrum as set from the preferences dialog for the peptide hit. More...
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void | addPeakAnnotationsFromID_ (const PeptideHit &hit) |
| Add peak annotatios from id data structure. More...
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void | removeTheoreticalSpectrumLayer_ () |
| removes all layer with theoretical spectrum generated in identification view More...
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void | removeGraphicalPeakAnnotations_ (int spectrum_index) |
| remove all graphical peak annotations More...
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void | addPeakAnnotations_ (const std::vector< PeptideIdentification > &ph) |
| Adds annotation (compound name, adducts, ppm error) to a peak in 1D spectra. More...
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String | n_times (Size n, String input) |
| Helper function for text formatting. More...
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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 sequence. More...
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template<typename SeqType > |
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. More...
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void | generateSequenceRow_ (const AASequence &seq, std::vector< String > &row) |
| Helper function for generateSequenceDiagram_() - overload for peptides. More...
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void | generateSequenceRow_ (const NASequence &seq, std::vector< String > &row) |
| Helper function for generateSequenceDiagram_() - overload for oligonucleotides. More...
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String | collapseStringVector (std::vector< String > strings) |
| Helper function, that collapses a vector of Strings into one String. More...
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Behavior of TOPPView in identification mode.