Behavior of TOPPView in identification mode. More...

#include <OpenMS/VISUAL/TVIdentificationViewController.h>

Inheritance diagram for TVIdentificationViewController:

Collaboration diagram for TVIdentificationViewController:

Public Slots
virtual void	showSpectrumAsNew1D (int spectrum_index, int peptide_id_index, int peptide_hit_index)
	Behavior for showSpectrumAsNew1D. More...

virtual void	showSpectrumAsNew1D (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...

void	activateBehavior () override
	Slot for behavior activation. More...

void	deactivateBehavior () override
	Slot for behavior deactivation. More...

void	setVisibleArea1D (double l, double h)

Public Slots inherited from TVControllerBase
virtual void	activateBehavior ()
	Slot for behavior activation. The default behaviour does nothing. Override in child class if desired. More...

virtual void	deactivateBehavior ()
	Slot for behavior deactivation. The default behaviour does nothing. Override in child class if desired. More...

Public Member Functions
	TVIdentificationViewController (TOPPViewBase parent, SpectraIDViewTab spec_id_view_)
	Construct the behaviour with its parent. More...

Public Member Functions inherited from TVControllerBase
	TVControllerBase ()=delete

virtual	~TVControllerBase ()=default

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	addPeakAnnotationsFromID_ (const PeptideHit &hit)
	Add peak annotatios from id data structure. More...

void	removeTheoreticalSpectrumLayer_ ()
	removes all layer with theoretical spectrum generated in identification view More...

void	removeGraphicalPeakAnnotations_ (int spectrum_index)
	remove all graphical peak annotations More...

void	addPeakAnnotations_ (const std::vector< PeptideIdentification > &ph)
	Adds annotation (compound name, adducts, ppm error) to a peak 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 visualization with the sequence. More...

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...

void	generateSequenceRow_ (const AASequence &seq, std::vector< String > &row)
	Helper function for generateSequenceDiagram_() - overload for peptides. More...

void	generateSequenceRow_ (const NASequence &seq, std::vector< String > &row)
	Helper function for generateSequenceDiagram_() - overload for oligonucleotides. More...

String	collapseStringVector (std::vector< String > strings)
	Helper function, that collapses a vector of Strings into one String. More...

Private Attributes
SpectraIDViewTab *	spec_id_view_

std::vector< Annotation1DItem * >	temporary_annotations_

Additional Inherited Members
Public Types inherited from TVControllerBase
typedef LayerData::FeatureMapType	FeatureMapType
	Feature map type. More...

typedef LayerData::FeatureMapSharedPtrType	FeatureMapSharedPtrType
	Feature map managed type. More...

typedef LayerData::ConsensusMapType	ConsensusMapType
	Consensus feature map type. More...

typedef LayerData::ConsensusMapSharedPtrType	ConsensusMapSharedPtrType
	Consensus map managed type. More...

typedef LayerData::ExperimentType	ExperimentType
	Peak map type. More...

typedef LayerData::ExperimentSharedPtrType	ExperimentSharedPtrType
	Main managed data type (experiment) More...

typedef ExperimentType::SpectrumType	SpectrumType
	Peak spectrum type. More...

Protected Member Functions inherited from TVControllerBase
	TVControllerBase (TOPPViewBase *parent)
	Construct the behaviour. More...

Protected Attributes inherited from TVControllerBase
TOPPViewBase *	tv_

Detailed Description

Behavior of TOPPView in identification mode.

Constructor & Destructor Documentation

◆ TVIdentificationViewController()

TVIdentificationViewController	(	TOPPViewBase *	parent,
		SpectraIDViewTab *	spec_id_view_
	)

Construct the behaviour with its parent.

Member Function Documentation

◆ activate1DSpectrum [1/2]

virtual void activate1DSpectrum ( int index )

virtualslot

select spectrum without selecting an identification

◆ activate1DSpectrum [2/2]

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

virtualslot

Behavior for activate1DSpectrum.

◆ activateBehavior

void activateBehavior ( )

overrideslot

Slot for behavior activation.

◆ addPeakAnnotations_()

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

private

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

◆ addPeakAnnotationsFromID_()

void addPeakAnnotationsFromID_ ( const PeptideHit & hit )

private

Add peak annotatios from id data structure.

◆ 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

void deactivateBehavior ( )

overrideslot

Slot for behavior deactivation.

◆ 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 visualization with the sequence.

◆ generateSequenceDiagram_()

String generateSequenceDiagram_	(	const SeqType &	seq,
		const std::vector< PeptideHit::PeakAnnotation > &	annotations,
		const StringList &	top_ions,
		const StringList &	bottom_ions
	)

private

Generates HTML for showing the sequence with annotations of matched fragments.

◆ generateSequenceRow_() [1/2]

void generateSequenceRow_	(	const AASequence &	seq,
		std::vector< String > &	row
	)

private

Helper function for generateSequenceDiagram_() - overload for peptides.

◆ generateSequenceRow_() [2/2]

void generateSequenceRow_	(	const NASequence &	seq,
		std::vector< String > &	row
	)

private

Helper function for generateSequenceDiagram_() - overload for oligonucleotides.

◆ n_times()

String n_times	(	Size	n,
		String	input
	)

private

Helper function for text formatting.

◆ removeGraphicalPeakAnnotations_()

void removeGraphicalPeakAnnotations_ ( int spectrum_index )

private

remove all graphical peak annotations

◆ 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

◆ showSpectrumAsNew1D [1/2]

virtual void showSpectrumAsNew1D ( int index )

virtualslot

Show spectrum without selecting an identification.

◆ showSpectrumAsNew1D [2/2]

virtual void showSpectrumAsNew1D	(	int	spectrum_index,
		int	peptide_id_index,
		int	peptide_hit_index
	)

virtualslot

Behavior for showSpectrumAsNew1D.

Member Data Documentation

◆ spec_id_view_

SpectraIDViewTab* spec_id_view_

private

◆ 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

Public Slots

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TVIdentificationViewController()

Member Function Documentation

◆ activate1DSpectrum [1/2]

◆ activate1DSpectrum [2/2]

◆ activateBehavior

◆ addPeakAnnotations_()

◆ addPeakAnnotationsFromID_()

◆ addPrecursorLabels1D_()

◆ addTheoreticalSpectrumLayer_()

◆ collapseStringVector()

◆ deactivate1DSpectrum

◆ deactivateBehavior

◆ extractCoverageStrings()

◆ generateSequenceDiagram_()

◆ generateSequenceRow_() [1/2]

◆ generateSequenceRow_() [2/2]

◆ n_times()

◆ removeGraphicalPeakAnnotations_()

◆ removeTemporaryAnnotations_()

◆ removeTheoreticalSpectrumLayer_()

◆ setVisibleArea1D

◆ showSpectrumAsNew1D [1/2]

◆ showSpectrumAsNew1D [2/2]

Member Data Documentation

◆ spec_id_view_

◆ temporary_annotations_