Class that stores the data for one layer of type PeakMap. More...

#include <OpenMS/VISUAL/LayerDataPeak.h>

Inheritance diagram for LayerDataPeak:

Collaboration diagram for LayerDataPeak:

Public Types
using	SpectrumType = ExperimentType::SpectrumType

using	PeakType = SpectrumType::PeakType

Public Types inherited from LayerDataBase
using	RangeAllType = RangeManager< RangeRT, RangeMZ, RangeIntensity, RangeMobility >

Public Types inherited from LayerDataDefs
enum	DataType { DT_PEAK , DT_CHROMATOGRAM , DT_FEATURE , DT_CONSENSUS , DT_IDENT , DT_UNKNOWN }

enum	Flags { F_HULL , F_HULLS , F_UNASSIGNED , P_PRECURSORS , P_PROJECTIONS , C_ELEMENTS , I_PEPTIDEMZ , I_LABELS , 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...

typedef boost::shared_ptr< const ExperimentType >	ConstExperimentSharedPtrType

typedef boost::shared_ptr< OnDiscMSExperiment >	ODExperimentSharedPtrType
	SharedPtr on On-Disc MSExperiment. More...

typedef boost::shared_ptr< OSWData >	OSWDataSharedPtrType
	SharedPtr on OSWData. More...

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

	LayerDataPeak (const LayerDataPeak &ld)=default
	Copy-ctor. More...

LayerDataPeak &	operator= (const LayerDataPeak &ld)=delete
	no assignment operator (should not be needed) More...

std::unique_ptr< Painter2DBase >	getPainter2D () const override
	Obtain a painter which can draw the layer on a 2D canvas. More...

std::unique_ptr< LayerData1DBase >	to1DLayer () const override
	Create a shallow copy (i.e. shared experimental data using shared_ptr) of the current layer, and make it 1D (i.e. support showing a single spec/chrom etc) More...

std::unique_ptr< LayerStoreData >	storeVisibleData (const RangeAllType &visible_range, const DataFilters &layer_filters) const override
	Returns a visitor which contains the current visible data and can write the data to disk. More...

std::unique_ptr< LayerStoreData >	storeFullData () const override
	Returns a visitor which contains the the full data of the layer and can write the data to disk in the appropriate format (e.g. mzML) More...

ProjectionData	getProjection (const DIM_UNIT unit_x, const DIM_UNIT unit_y, const RangeAllType &area) const override

PeakIndex	findHighestDataPoint (const RangeAllType &area) const override
	Find the datapoint with the highest intensity within the given range and return a proxy to that datapoint. More...

void	updateRanges () override
	Update ranges of the underlying data. More...

RangeAllType	getRange () const override

PointXYType	peakIndexToXY (const PeakIndex &peak, const DimMapper< 2 > &mapper) const override
	Convert a PeakIndex to a XY coordinate (via `mapper`). More...

String	getDataArrayDescription (const PeakIndex &peak_index) override
	Get name and value of all data-arrays corresponding to the given datapoint. More...

std::unique_ptr< LayerStatistics >	getStats () const override
	Compute layer statistics (via visitor) More...

bool	annotate (const std::vector< PeptideIdentification > &identifications, const std::vector< ProteinIdentification > &protein_identifications) override

const ExperimentType::SpectrumType &	getSpectrum (Size spectrum_idx) const

const ConstExperimentSharedPtrType	getPeakData () const
	Returns a const reference to the current in-memory peak data. More...

const ExperimentSharedPtrType &	getPeakDataMuteable ()
	Returns a mutable reference to the current in-memory peak data. More...

void	setPeakData (ExperimentSharedPtrType p)
	Set the current in-memory peak data. More...

void	setOnDiscPeakData (ODExperimentSharedPtrType p)
	Set the current on-disc data. More...

const ODExperimentSharedPtrType &	getOnDiscPeakData () const
	Returns a mutable reference to the on-disc data. More...

bool	isIonMobilityData () const
	Check whether the current layer should be represented as ion mobility. More...

void	labelAsIonMobilityData () const

bool	isDIAData () const
	Check whether the current layer contains DIA (SWATH-MS) data. More...

void	labelAsDIAData ()
	Label the current layer as DIA (SWATH-MS) data. More...

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

void	set_chromatogram_flag ()
	set the chromatogram flag More...

void	remove_chromatogram_flag ()
	remove the chromatogram flag More...

Public Member Functions inherited from LayerDataBase
	LayerDataBase ()=delete
	Default constructor (for virtual inheritance) More...

	LayerDataBase (const DataType type)
	C'tor for child classes. More...

	LayerDataBase (const LayerDataBase &ld)=default
	Copy-C'tor. More...

LayerDataBase &	operator= (const LayerDataBase &ld)=delete
	Assignment operator. More...

	LayerDataBase (LayerDataBase &&ld)=delete

LayerDataBase &	operator= (LayerDataBase &&ld)=delete
	Move assignment – deleted, by same argument as for move c'tor. More...

virtual	~LayerDataBase ()=default
	D'tor. More...

virtual PeakIndex	findClosestDataPoint (const RangeAllType &) const
	Find the closest datapoint within the given range and return a proxy to that datapoint. More...

float	getMinIntensity () const
	Returns the minimum intensity of the internal data, depending on type. More...

float	getMaxIntensity () const
	Returns the maximum intensity of the internal data, depending on type. More...

const String &	getName () const
	The name of the layer, usually the basename of the file. More...

void	setName (const String &new_name)
	Set the name of the layer, usually the basename of the file. More...

const String &	getNameSuffix () const
	get the extra annotation to the layers name, e.g. '[39]' for which chromatogram index is currently shown in 1D More...

void	setNameSuffix (const String &decorator)
	set an extra annotation as suffix to the layers name, e.g. '[39]' for which chromatogram index is currently shown in 1D More...

virtual String	getDecoratedName () const
	get name augmented with attributes, e.g. '*' if modified More...

Protected Attributes
ExperimentSharedPtrType	peak_map_ = ExperimentSharedPtrType(new ExperimentType())
	peak data More...

ODExperimentSharedPtrType	on_disc_peaks_ = ODExperimentSharedPtrType(new OnDiscMSExperiment())
	on disc peak data More...

Additional Inherited Members
Public Attributes inherited from LayerDataBase
std::bitset< SIZE_OF_FLAGS >	flags
	Actual state of each flag. More...

bool	visible = true
	if this layer is visible More...

DataType	type = DT_UNKNOWN
	data type (peak or feature data, etc) More...

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

Param	param
	Layer parameters. More...

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

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

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

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

LabelType	label = L_NONE
	Label type. More...

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

int	peptide_hit_index = -1

Static Public Attributes inherited from LayerDataDefs
static const std::string	NamesOfLabelType [SIZE_OF_LABEL_TYPE]
	Label names. More...

Detailed Description

Class that stores the data for one layer of type PeakMap.

Member Typedef Documentation

◆ PeakType

using PeakType = SpectrumType::PeakType

◆ SpectrumType

using SpectrumType = ExperimentType::SpectrumType

Constructor & Destructor Documentation

◆ LayerDataPeak() [1/2]

LayerDataPeak ( )

Default constructor.

◆ LayerDataPeak() [2/2]

LayerDataPeak ( const LayerDataPeak & ld )

default

Copy-ctor.

Member Function Documentation

◆ annotate()

bool annotate	(	const std::vector< PeptideIdentification > &	identifications,
		const std::vector< ProteinIdentification > &	protein_identifications
	)

overridevirtual

add peptide identifications to the layer Only supported for DT_PEAK, DT_FEATURE and DT_CONSENSUS. Will return false otherwise.

Reimplemented from LayerDataBase.

◆ chromatogram_flag_set()

bool chromatogram_flag_set ( ) const

inline

Check whether the current layer is a chromatogram.

This is needed because type will *not* distinguish properly between chromatogram and spectra data. This is due to the fact that we store chromatograms for display in 1D in a data layer using MSSpectrum and so the layer looks like PEAK data to tools.

◆ findHighestDataPoint()

PeakIndex findHighestDataPoint ( const RangeAllType & ) const

overridevirtual

Find the datapoint with the highest intensity within the given range and return a proxy to that datapoint.

Parameters

area	Range to search in. Only dimensions used in the canvas are populated.

Returns: A proxy (e.g. scan + peak index in an MSExperiment) which points to the data

Reimplemented from LayerDataBase.

◆ getDataArrayDescription()

String getDataArrayDescription ( const PeakIndex & )

overridevirtual

Get name and value of all data-arrays corresponding to the given datapoint.

Empty (or shorter) data-arrays are skipped.

Parameters

peak_index The datapoint

Returns: A string, e.g. "fwhm: 20, im: 3.3", depending on which float/string dataarrays are populated for the given datapoint

Reimplemented from LayerDataBase.

◆ getOnDiscPeakData()

const ODExperimentSharedPtrType& getOnDiscPeakData ( ) const

inline

Returns a mutable reference to the on-disc data.

◆ getPainter2D()

std::unique_ptr<Painter2DBase> getPainter2D ( ) const

overridevirtual

Obtain a painter which can draw the layer on a 2D canvas.

Returns: A painter

Implements LayerDataBase.

◆ getPeakData()

const ConstExperimentSharedPtrType getPeakData ( ) const

Returns a const reference to the current in-memory peak data.

Note: Depending on the caching strategy (on-disk or in-memory), all or some spectra may have zero size and contain only meta data since peak data is cached on disk.; Do *not* use this function to access the current spectrum for the 1D view, use getCurrentSpectrum() instead.

◆ getPeakDataMuteable()

const ExperimentSharedPtrType& getPeakDataMuteable ( )

inline

Returns a mutable reference to the current in-memory peak data.

Note: Depending on the caching strategy (on-disk or in-memory), all or some spectra may have zero size and contain only meta data since peak data is cached on disk.; Do *not* use this function to access the current spectrum for the 1D view, use getCurrentSpectrum() instead.

Referenced by TOPPViewBase::showCurrentPeaksAs2D().

◆ getProjection()

ProjectionData getProjection	(	const DIM_UNIT	unit_x,
		const DIM_UNIT	unit_y,
		const RangeAllType &	area
	)		const

overridevirtual

Calculate a projection of the current layer for the given unit and the given area. E.g. the area might be restricted in RT and m/z, and then requested projection should return the XIC (unit == RT) It is up to the implementation to decide on binning.

Implements LayerDataBase.

◆ getRange()

RangeAllType getRange ( ) const

inlineoverridevirtual

Returns the data range of the whole layer (i.e. all scans/chroms/etc) in all known dimensions. If a layer does not support the dimension (or the layer is empty) the dimension will be empty If you need the data range for a 1D view (i.e. only a single spec/chrom/etc), call 'LayerDataBase1D::getRange1D()'

Implements LayerDataBase.

References RangeManager< RangeBases >::assign().

◆ getSpectrum()

const ExperimentType::SpectrumType& getSpectrum ( Size spectrum_idx ) const

inline

Referenced by LayerData1DPeak::getCurrentSpectrum().

◆ getStats()

std::unique_ptr<LayerStatistics> getStats ( ) const

overridevirtual

Compute layer statistics (via visitor)

Implements LayerDataBase.

◆ isDIAData()

bool isDIAData ( ) const

inline

Check whether the current layer contains DIA (SWATH-MS) data.

◆ isIonMobilityData()

bool isIonMobilityData ( ) const

inline

Check whether the current layer should be represented as ion mobility.

◆ labelAsDIAData()

void labelAsDIAData ( )

inline

Label the current layer as DIA (SWATH-MS) data.

◆ labelAsIonMobilityData()

void labelAsIonMobilityData ( ) const

inline

◆ operator=()

LayerDataPeak& operator= ( const LayerDataPeak & ld )

delete

no assignment operator (should not be needed)

◆ peakIndexToXY()

PointXYType peakIndexToXY	(	const PeakIndex &	peak,
		const DimMapper< 2 > &	mapper
	)		const

overridevirtual

Convert a PeakIndex to a XY coordinate (via mapper).

Parameters

peak	The Peak to convert
mapper	Converts the internal representation (e.g. Peak1D) to an XY coordinate

Returns: XY coordinate in data units (e.g. X=m/z, Y=intensity)

Implements LayerDataBase.

◆ remove_chromatogram_flag()

void remove_chromatogram_flag ( )

inline

remove the chromatogram flag

◆ set_chromatogram_flag()

void set_chromatogram_flag ( )

inline

set the chromatogram flag

◆ setOnDiscPeakData()

void setOnDiscPeakData ( ODExperimentSharedPtrType p )

inline

Set the current on-disc data.

◆ setPeakData()

void setPeakData ( ExperimentSharedPtrType p )

inline

Set the current in-memory peak data.

◆ storeFullData()

std::unique_ptr<LayerStoreData> storeFullData ( ) const

overridevirtual

Returns a visitor which contains the the full data of the layer and can write the data to disk in the appropriate format (e.g. mzML)

Reimplemented from LayerDataBase.

◆ storeVisibleData()

std::unique_ptr<LayerStoreData> storeVisibleData	(	const RangeAllType &	,
		const DataFilters &
	)		const

overridevirtual

Returns a visitor which contains the current visible data and can write the data to disk.

Reimplemented from LayerDataBase.

◆ to1DLayer()

std::unique_ptr<LayerData1DBase> to1DLayer ( ) const

overridevirtual

Create a shallow copy (i.e. shared experimental data using shared_ptr) of the current layer, and make it 1D (i.e. support showing a single spec/chrom etc)

Returns: A new layer for 1D

Implements LayerDataBase.

◆ updateRanges()

void updateRanges ( )

inlineoverridevirtual

Update ranges of the underlying data.

Implements LayerDataBase.

Referenced by LayerData1DPeak::updateRanges().

Member Data Documentation

◆ on_disc_peaks_

ODExperimentSharedPtrType on_disc_peaks_ = ODExperimentSharedPtrType(new OnDiscMSExperiment())

protected

on disc peak data

◆ peak_map_

ExperimentSharedPtrType peak_map_ = ExperimentSharedPtrType(new ExperimentType())

protected

peak data

Public Types

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ PeakType

◆ SpectrumType

Constructor & Destructor Documentation

◆ LayerDataPeak() [1/2]

◆ LayerDataPeak() [2/2]

Member Function Documentation

◆ annotate()

◆ chromatogram_flag_set()

◆ findHighestDataPoint()

◆ getDataArrayDescription()

◆ getOnDiscPeakData()

◆ getPainter2D()

◆ getPeakData()

◆ getPeakDataMuteable()

◆ getProjection()

◆ getRange()

◆ getSpectrum()

◆ getStats()

◆ isDIAData()

◆ isIonMobilityData()

◆ labelAsDIAData()

◆ labelAsIonMobilityData()

◆ operator=()

◆ peakIndexToXY()

◆ remove_chromatogram_flag()

◆ set_chromatogram_flag()

◆ setOnDiscPeakData()

◆ setPeakData()

◆ storeFullData()

◆ storeVisibleData()

◆ to1DLayer()

◆ updateRanges()

Member Data Documentation

◆ on_disc_peaks_

◆ peak_map_