Class that stores the data for one layer. More...

#include <OpenMS/VISUAL/LayerData.h>

Public Member Functions
	LayerData ()
	Default constructor. More...

const ExperimentType::SpectrumType &	getCurrentSpectrum () const
	Returns a const reference to the current spectrum (1d view) More...

const FeatureMapSharedPtrType &	getFeatureMap () const
	Returns a const reference to the current feature data. More...

FeatureMapSharedPtrType &	getFeatureMap ()
	Returns a const reference to the current feature data. More...

const ConsensusMapSharedPtrType &	getConsensusMap () const
	Returns a const reference to the consensus feature data. More...

ConsensusMapSharedPtrType &	getConsensusMap ()
	Returns current consensus map (mutable) More...

const ExperimentSharedPtrType &	getPeakData () const
	Returns a const reference to the current peak data. More...

ExperimentSharedPtrType &	getPeakData ()
	Returns a mutable reference to the current peak data. More...

const ExperimentSharedPtrType &	getChromatogramData () const
	Returns a const reference to the current chromatogram data. More...

ExperimentSharedPtrType &	getChromatogramData ()
	Returns a mutable reference to the current chromatogram data. More...

const Annotations1DContainer &	getCurrentAnnotations () const
	Returns a const reference to the annotations of the current spectrum (1d view) More...

Annotations1DContainer &	getCurrentAnnotations ()
	Returns a mutable reference to the annotations of the current spectrum (1d view) More...

const Annotations1DContainer &	getAnnotations (Size spectrum_index) const
	Returns a const reference to the annotations of the current spectrum (1d view) More...

Annotations1DContainer &	getAnnotations (Size spectrum_index)
	Returns a mutable reference to the annotations of the current spectrum (1d view) More...

ExperimentType::SpectrumType &	getCurrentSpectrum ()
	Returns a mutable reference to the current spectrum (1d view) More...

Size	getCurrentSpectrumIndex () const
	Get the index of the current spectrum. More...

void	setCurrentSpectrumIndex (Size index)
	Set the index of the current spectrum. More...

bool	chromatogram_flag_set () const
	Check whether the current layer is a chromatogram. More...

void	set_chromatogram_flag ()

void	remove_chromatogram_flag ()

void	synchronizePeakAnnotations ()

void	removePeakAnnotationsFromPeptideHit (const std::vector< Annotation1DItem *> &selected_annotations)
	remove peak annotations in the given list from the currently active PeptideHit More...

Public Attributes
bool	visible
	if this layer is visible More...

bool	flipped
	if this layer is flipped (1d mirror view) More...

DataType	type
	data type (peak or feature data) More...

String	name
	layer name More...

String	filename
	file name of the file the data comes from (if available) More...

std::vector< PeptideIdentification >	peptides
	peptide identifications More...

Param	param
	Layer parameters. More...

MultiGradient	gradient
	Gradient for 2D and 3D views. More...

DataFilters	filters
	Filters to apply before painting. More...

std::vector< Annotations1DContainer >	annotations_1d
	Annotations of all spectra of the experiment (1D view) More...

bool	modifiable
	Flag that indicates if the layer data can be modified (so far used for features only) More...

bool	modified
	Flag that indicates that the layer data was modified since loading it. More...

LabelType	label
	Label type. More...

int	peptide_id_index
	Selected peptide id and hit index (-1 if none is selected) More...

int	peptide_hit_index

Private Member Functions
void	updatePeptideHitAnnotations_ (PeptideHit &hit)
	updates the PeakAnnotations in the current PeptideHit with manually changed annotations More...

Private Attributes
FeatureMapSharedPtrType	features
	feature data More...

ConsensusMapSharedPtrType	consensus
	consensus feature data More...

ExperimentSharedPtrType	peaks
	peak data More...

ExperimentSharedPtrType	chromatograms
	chromatogram data More...

Size	current_spectrum_
	Index of the current spectrum. More...

Type definitions
enum	DataType { DT_PEAK, DT_FEATURE, DT_CONSENSUS, DT_CHROMATOGRAM, DT_IDENT, DT_UNKNOWN }
	Dataset types. More...

enum	Flags { F_HULL, F_HULLS, F_UNASSIGNED, P_PRECURSORS, P_PROJECTIONS, C_ELEMENTS, I_PEPTIDEMZ, SIZE_OF_FLAGS }
	Flags that determine which information is shown. More...

enum	LabelType { L_NONE, L_INDEX, L_META_LABEL, L_ID, L_ID_ALL, SIZE_OF_LABEL_TYPE }
	Label used in visualization. More...

typedef FeatureMap	FeatureMapType
	Features. More...

typedef boost::shared_ptr< FeatureMap >	FeatureMapSharedPtrType
	SharedPtr on feature map. More...

typedef ConsensusMap	ConsensusMapType
	consensus features More...

typedef boost::shared_ptr< ConsensusMap >	ConsensusMapSharedPtrType
	SharedPtr on consensus features. More...

typedef PeakMap	ExperimentType
	Main data type (experiment) More...

typedef boost::shared_ptr< ExperimentType >	ExperimentSharedPtrType
	SharedPtr on MSExperiment. More...

std::bitset< SIZE_OF_FLAGS >	flags
	Actual state of each flag. More...

static const std::string	NamesOfLabelType [SIZE_OF_LABEL_TYPE]
	Label names. More...

Detailed Description

Class that stores the data for one layer.

Member Typedef Documentation

◆ ConsensusMapSharedPtrType

typedef boost::shared_ptr<ConsensusMap> ConsensusMapSharedPtrType

SharedPtr on consensus features.

◆ ConsensusMapType

typedef ConsensusMap ConsensusMapType

consensus features

◆ ExperimentSharedPtrType

typedef boost::shared_ptr<ExperimentType> ExperimentSharedPtrType

SharedPtr on MSExperiment.

◆ ExperimentType

typedef PeakMap ExperimentType

Main data type (experiment)

◆ FeatureMapSharedPtrType

typedef boost::shared_ptr<FeatureMap > FeatureMapSharedPtrType

SharedPtr on feature map.

◆ FeatureMapType

typedef FeatureMap FeatureMapType

Features.

Member Enumeration Documentation

◆ DataType

enum DataType

Dataset types.

Enumerator
DT_PEAK	Spectrum profile or centroided data.
DT_FEATURE	Feature data.
DT_CONSENSUS	Consensus feature data.
DT_CHROMATOGRAM	Chromatogram data.
DT_IDENT	Peptide identification data.
DT_UNKNOWN	Undefined data type indicating an error.

◆ Flags

enum Flags

Flags that determine which information is shown.

Enumerator
F_HULL	Features: Overall convex hull.
F_HULLS	Features: Convex hulls of single mass traces.
F_UNASSIGNED	Features: Unassigned peptide hits.
P_PRECURSORS	Peaks: Mark precursor peaks of MS/MS scans.
P_PROJECTIONS	Peaks: Show projections.
C_ELEMENTS	Consensus features: Show elements.
I_PEPTIDEMZ	Identifications: m/z source.
SIZE_OF_FLAGS

◆ LabelType

enum LabelType

Label used in visualization.

Enumerator
L_NONE	No label is displayed.
L_INDEX	The element number is used.
L_META_LABEL	The 'label' meta information is used.
L_ID	The best peptide hit of the first identification run is used.
L_ID_ALL	All peptide hits of the first identification run are used.
SIZE_OF_LABEL_TYPE

Constructor & Destructor Documentation

◆ LayerData()

LayerData ( )

inline

Default constructor.

References LayerData::annotations_1d, and LayerData::getCurrentSpectrum().

Member Function Documentation

◆ chromatogram_flag_set()

bool chromatogram_flag_set ( ) const

inline

Check whether the current layer is a chromatogram.

References LayerData::getPeakData().

Referenced by LayerData::remove_chromatogram_flag(), and TOPPViewBase::runTOPPTool_().

◆ getAnnotations() [1/2]

const Annotations1DContainer& getAnnotations ( Size spectrum_index ) const

inline

Returns a const reference to the annotations of the current spectrum (1d view)

References LayerData::annotations_1d.

◆ getAnnotations() [2/2]

Annotations1DContainer& getAnnotations ( Size spectrum_index )

inline

Returns a mutable reference to the annotations of the current spectrum (1d view)

References LayerData::annotations_1d.

◆ getChromatogramData() [1/2]

const ExperimentSharedPtrType& getChromatogramData ( ) const

inline

Returns a const reference to the current chromatogram data.

References LayerData::chromatograms.

◆ getChromatogramData() [2/2]

ExperimentSharedPtrType& getChromatogramData ( )

inline

Returns a mutable reference to the current chromatogram data.

References LayerData::chromatograms.

◆ getConsensusMap() [1/2]

const ConsensusMapSharedPtrType& getConsensusMap ( ) const

inline

Returns a const reference to the consensus feature data.

References LayerData::consensus.

Referenced by TOPPViewBase::annotateWithID(), TOPPViewBase::copyLayer(), TOPPViewBase::fileChanged_(), and TOPPViewBase::runTOPPTool_().

◆ getConsensusMap() [2/2]

ConsensusMapSharedPtrType& getConsensusMap ( )

inline

Returns current consensus map (mutable)

References LayerData::consensus.

◆ getCurrentAnnotations() [1/2]

const Annotations1DContainer& getCurrentAnnotations ( ) const

inline

Returns a const reference to the annotations of the current spectrum (1d view)

References LayerData::annotations_1d, and LayerData::current_spectrum_.

◆ getCurrentAnnotations() [2/2]

Annotations1DContainer& getCurrentAnnotations ( )

inline

Returns a mutable reference to the annotations of the current spectrum (1d view)

References LayerData::annotations_1d, and LayerData::current_spectrum_.

◆ getCurrentSpectrum() [1/2]

const ExperimentType::SpectrumType& getCurrentSpectrum ( ) const

Returns a const reference to the current spectrum (1d view)

Referenced by LayerData::LayerData().

◆ getCurrentSpectrum() [2/2]

ExperimentType::SpectrumType& getCurrentSpectrum ( )

inline

Returns a mutable reference to the current spectrum (1d view)

References LayerData::current_spectrum_, and LayerData::peaks.

◆ getCurrentSpectrumIndex()

Size getCurrentSpectrumIndex ( ) const

inline

Get the index of the current spectrum.

References LayerData::current_spectrum_.

Referenced by TOPPViewBase::runTOPPTool_().

◆ getFeatureMap() [1/2]

const FeatureMapSharedPtrType& getFeatureMap ( ) const

inline

Returns a const reference to the current feature data.

References LayerData::features.

Referenced by TOPPViewBase::annotateWithID(), TOPPViewBase::copyLayer(), TOPPViewBase::fileChanged_(), and TOPPViewBase::runTOPPTool_().

◆ getFeatureMap() [2/2]

FeatureMapSharedPtrType& getFeatureMap ( )

inline

Returns a const reference to the current feature data.

References LayerData::features.

◆ getPeakData() [1/2]

const ExperimentSharedPtrType& getPeakData ( ) const

inline

Returns a const reference to the current peak data.

References LayerData::peaks.

Referenced by TOPPViewBase::addData(), TOPPViewBase::annotateMS1FromMassFingerprinting_(), TOPPViewBase::annotateWithID(), LayerData::chromatogram_flag_set(), TOPPViewBase::copyLayer(), TOPPViewBase::enhancedWorkspaceWindowChanged(), TOPPViewBase::fileChanged_(), TOPPViewBase::layerZoomChanged(), LayerData::remove_chromatogram_flag(), TOPPViewBase::runTOPPTool_(), LayerData::set_chromatogram_flag(), TOPPViewBase::showCurrentPeaksAs2D(), and TOPPViewBase::showCurrentPeaksAs3D().

◆ getPeakData() [2/2]

ExperimentSharedPtrType& getPeakData ( )

inline

Returns a mutable reference to the current peak data.

References LayerData::peaks.

◆ remove_chromatogram_flag()

void remove_chromatogram_flag ( )

inline

References LayerData::chromatogram_flag_set(), LayerData::getPeakData(), LayerData::removePeakAnnotationsFromPeptideHit(), and LayerData::synchronizePeakAnnotations().

Referenced by TOPPViewBase::runTOPPTool_().

◆ removePeakAnnotationsFromPeptideHit()

void removePeakAnnotationsFromPeptideHit ( const std::vector< Annotation1DItem *> & selected_annotations )

remove peak annotations in the given list from the currently active PeptideHit

Referenced by LayerData::remove_chromatogram_flag().

◆ set_chromatogram_flag()

void set_chromatogram_flag ( )

inline

References LayerData::getPeakData().

◆ setCurrentSpectrumIndex()

void setCurrentSpectrumIndex ( Size index )

inline

Set the index of the current spectrum.

References LayerData::current_spectrum_.

◆ synchronizePeakAnnotations()

void synchronizePeakAnnotations ( )

updates the PeakAnnotations in the current PeptideHit with manually changed annotations if no PeptideIdentification or PeptideHit for the spectrum exist, it is generated

Referenced by LayerData::remove_chromatogram_flag().