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TOPPViewIdentificationViewBehavior Class Reference

Behavior of TOPPView in identification mode. More...

#include <OpenMS/VISUAL/TOPPViewIdentificationViewBehavior.h>

Inheritance diagram for TOPPViewIdentificationViewBehavior:
QObject

Public Slots

virtual void showSpectrumAs1D (int spectrum_index, int peptide_id_index, int peptide_hit_index)
 Behavior for showSpectrumAs1D. More...
 
virtual void showSpectrumAs1D (int index)
 Show spectrum without selecting an identification. More...
 
virtual void activate1DSpectrum (int spectrum_index, int peptide_id_index, int peptide_hit_index)
 Behavior for activate1DSpectrum. More...
 
virtual void activate1DSpectrum (int index)
 select spectrum without selecting an identification More...
 
virtual void deactivate1DSpectrum (int index)
 Behavior for deactivate1DSpectrum. More...
 
virtual void activateBehavior ()
 Slot for behavior activation. More...
 
virtual void deactivateBehavior ()
 Slot for behavior deactivation. More...
 
void setVisibleArea1D (double l, double h)
 

Public Member Functions

 TOPPViewIdentificationViewBehavior (TOPPViewBase *parent)
 Construct the behaviour with its parent. More...
 

Private Types

Type definitions
typedef LayerData::FeatureMapType FeatureMapType
 
typedef LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType
 
typedef LayerData::ConsensusMapType ConsensusMapType
 
typedef LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType
 
typedef LayerData::ExperimentType ExperimentType
 
typedef LayerData::ExperimentSharedPtrType ExperimentSharedPtrType
 
typedef ExperimentType::SpectrumType SpectrumType
 Peak spectrum type. More...
 

Private Member Functions

void addPrecursorLabels1D_ (const std::vector< Precursor > &pcs)
 Adds labels for the provided precursors to the 1D spectrum. More...
 
void removeTemporaryAnnotations_ (Size spectrum_index)
 Removes the precursor labels for from the specified 1D spectrum. More...
 
void addTheoreticalSpectrumLayer_ (const PeptideHit &ph)
 Adds a theoretical spectrum as set from the preferences dialog for the peptide hit. More...
 
void removeTheoreticalSpectrumLayer_ ()
 removes all layer with theoretical spectrum generated in identification view More...
 
void addPeakAnnotations_ (const std::vector< PeptideIdentification > &ph)
 Adds annotation (compound name, adducts, ppm error) to a peak in 1D spectra. More...
 
void addFragmentAnnotations_ (const PeptideHit &ph)
 Adds fragment annotations to peaks in 1D spectra. More...
 
String n_times (Size n, String input)
 Helper function for text formatting. More...
 
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 visuaization with the sequence. More...
 
String collapseStringVector (std::vector< String > strings)
 Helper function, that collapses a vector of Strings into one String. More...
 

Private Attributes

TOPPViewBasetv_
 
std::vector< Annotation1DItem * > temporary_annotations_
 

Detailed Description

Behavior of TOPPView in identification mode.

Member Typedef Documentation

◆ ConsensusMapSharedPtrType

◆ ConsensusMapType

◆ ExperimentSharedPtrType

◆ ExperimentType

◆ FeatureMapSharedPtrType

◆ FeatureMapType

◆ SpectrumType

Peak spectrum type.

Constructor & Destructor Documentation

◆ TOPPViewIdentificationViewBehavior()

Construct the behaviour with its parent.

Member Function Documentation

◆ activate1DSpectrum [1/2]

virtual void activate1DSpectrum ( int  spectrum_index,
int  peptide_id_index,
int  peptide_hit_index 
)
virtualslot

Behavior for activate1DSpectrum.

◆ activate1DSpectrum [2/2]

virtual void activate1DSpectrum ( int  index)
virtualslot

select spectrum without selecting an identification

◆ activateBehavior

virtual void activateBehavior ( )
virtualslot

Slot for behavior activation.

Referenced by TOPPViewBase::viewChanged().

◆ addFragmentAnnotations_()

void addFragmentAnnotations_ ( const PeptideHit ph)
private

Adds fragment annotations to peaks in 1D spectra.

◆ addPeakAnnotations_()

void addPeakAnnotations_ ( const std::vector< PeptideIdentification > &  ph)
private

Adds annotation (compound name, adducts, ppm error) to a peak in 1D spectra.

◆ addPrecursorLabels1D_()

void addPrecursorLabels1D_ ( const std::vector< Precursor > &  pcs)
private

Adds labels for the provided precursors to the 1D spectrum.

◆ addTheoreticalSpectrumLayer_()

void addTheoreticalSpectrumLayer_ ( const PeptideHit ph)
private

Adds a theoretical spectrum as set from the preferences dialog for the peptide hit.

◆ collapseStringVector()

String collapseStringVector ( std::vector< String strings)
private

Helper function, that collapses a vector of Strings into one String.

◆ deactivate1DSpectrum

virtual void deactivate1DSpectrum ( int  index)
virtualslot

Behavior for deactivate1DSpectrum.

◆ deactivateBehavior

virtual void deactivateBehavior ( )
virtualslot

Slot for behavior deactivation.

Referenced by TOPPViewBase::viewChanged().

◆ extractCoverageStrings()

void extractCoverageStrings ( std::vector< PeptideHit::PeakAnnotation frag_annotations,
String alpha_string,
String beta_string,
Size  alpha_size,
Size  beta_size 
)
private

Helper function, that turns fragment annotations into coverage Strings for visuaization with the sequence.

◆ n_times()

String n_times ( Size  n,
String  input 
)
private

Helper function for text formatting.

◆ removeTemporaryAnnotations_()

void removeTemporaryAnnotations_ ( Size  spectrum_index)
private

Removes the precursor labels for from the specified 1D spectrum.

◆ removeTheoreticalSpectrumLayer_()

void removeTheoreticalSpectrumLayer_ ( )
private

removes all layer with theoretical spectrum generated in identification view

◆ setVisibleArea1D

void setVisibleArea1D ( double  l,
double  h 
)
slot

◆ showSpectrumAs1D [1/2]

virtual void showSpectrumAs1D ( int  spectrum_index,
int  peptide_id_index,
int  peptide_hit_index 
)
virtualslot

Behavior for showSpectrumAs1D.

Referenced by TOPPViewBase::showSpectrumAs1D().

◆ showSpectrumAs1D [2/2]

virtual void showSpectrumAs1D ( int  index)
virtualslot

Show spectrum without selecting an identification.

Member Data Documentation

◆ temporary_annotations_

std::vector<Annotation1DItem *> temporary_annotations_
private

Used to check which annotation handles have been added automatically by the identification view. Ownership of the AnnotationItems has the Annotation1DContainer

◆ tv_

TOPPViewBase* tv_
private

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:14 using doxygen 1.8.13