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

#include <OpenMS/VISUAL/LayerDataBase.h>

Inheritance diagram for LayerDataBase:

Collaboration diagram for LayerDataBase:

Public Types
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
	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 std::unique_ptr< Painter2DBase >	getPainter2D () const =0
	Obtain a painter which can draw the layer on a 2D canvas. More...

virtual std::unique_ptr< LayerData1DBase >	to1DLayer () const =0
	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...

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

virtual std::unique_ptr< LayerStoreData >	storeFullData () const
	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...

virtual ProjectionData	getProjection (const DIM_UNIT unit_x, const DIM_UNIT unit_y, const RangeAllType &area) const =0

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

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

virtual PointXYType	peakIndexToXY (const PeakIndex &peak, const DimMapper< 2 > &mapper) const =0
	Convert a PeakIndex to a XY coordinate (via `mapper`). More...

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

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

virtual void	updateRanges ()=0
	Update ranges of the underlying data. 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...

virtual RangeAllType	getRange () const =0

virtual std::unique_ptr< LayerStatistics >	getStats () const =0
	Compute layer statistics (via visitor) 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...

Public Attributes
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

Private Attributes
String	name_
	layer name More...

String	name_suffix_
	an extra annotation as suffix to the layers name, e.g. '[39]' for which chromatogram index is currently shown in 1D More...

Additional Inherited Members
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.

The data for a layer can be peak data, feature data (feature, consensus), chromatogram or peptide identification data.

For 2D and 3D data, the data is generally accessible through getPeakData() while features are accessible through getFeatureMap() and getConsensusMap(). For 1D data, the current spectrum must be accessed through getCurrentSpectrum().

Peak data is stored using a shared pointer to an MSExperiment data structure as well as a shared pointer to a OnDiscMSExperiment data structure. Note that the actual data may not be in memory as this is not efficient for large files and therefore may have to be retrieved from disk on-demand.

Note: The spectrum for 1D viewing retrieved through getCurrentSpectrum() is a copy of the actual raw data and *different* from the one retrieved through getPeakData()[index]. Any changes to applied to getCurrentSpectrum() are non-persistent and will be gone the next time the cache is updated. Persistent changes can be applied to getPeakDataMuteable() and will be available on the next cache update.; Layer is mainly used as a member variable of PlotCanvas which holds a vector of LayerDataBase objects.

Member Typedef Documentation

◆ RangeAllType

using RangeAllType = RangeManager<RangeRT, RangeMZ, RangeIntensity, RangeMobility>

Constructor & Destructor Documentation

◆ LayerDataBase() [1/4]

LayerDataBase ( )

delete

Default constructor (for virtual inheritance)

◆ LayerDataBase() [2/4]

LayerDataBase ( const DataType type )

inlineexplicit

C'tor for child classes.

◆ LayerDataBase() [3/4]

LayerDataBase ( const LayerDataBase & ld )

default

Copy-C'tor.

◆ LayerDataBase() [4/4]

LayerDataBase ( LayerDataBase && ld )

delete

Move-C'tor - do not move from this class since its a virtual base class (diamond problem) and the move c'tor may be called twice (which would loose data!) Instead of painstakingly writing user-defined move c'tors which check for moving for all the direct child classes, we'd rather use copy (which is the automatic fallback, and safe) and incur a small performance hit

◆ ~LayerDataBase()

virtual ~LayerDataBase ( )

virtualdefault

D'tor.

Member Function Documentation

◆ annotate()

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

virtual

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

Reimplemented in LayerDataPeak, LayerDataFeature, and LayerDataConsensus.

◆ findClosestDataPoint()

virtual PeakIndex findClosestDataPoint ( const RangeAllType & ) const

inlinevirtual

Find the closest datapoint 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 in LayerData1DPeak, LayerData1DIonMobility, and LayerData1DChrom.

◆ findHighestDataPoint()

virtual PeakIndex findHighestDataPoint ( const RangeAllType & ) const

inlinevirtual

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 in LayerDataPeak, LayerDataFeature, LayerDataConsensus, LayerDataChrom, LayerDataIonMobility, and LayerDataIdent.

◆ getDataArrayDescription()

virtual String getDataArrayDescription ( const PeakIndex & )

inlinevirtual

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 in LayerDataPeak, LayerDataIonMobility, and LayerDataChrom.

◆ getDecoratedName()

virtual String getDecoratedName ( ) const

virtual

get name augmented with attributes, e.g. '*' if modified

Reimplemented in LayerData1DBase.

Referenced by TOPPViewBase::showPlotWidgetInWindow().

◆ getMaxIntensity()

float getMaxIntensity ( ) const

Returns the maximum intensity of the internal data, depending on type.

◆ getMinIntensity()

float getMinIntensity ( ) const

Returns the minimum intensity of the internal data, depending on type.

◆ getName()

const String& getName ( ) const

inline

The name of the layer, usually the basename of the file.

Referenced by TOPPViewBase::addData(), TOPPViewBase::copyLayer(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAsDIA(), and TOPPViewBase::showTOPPDialog_().

◆ getNameSuffix()

const String& getNameSuffix ( ) const

inline

get the extra annotation to the layers name, e.g. '[39]' for which chromatogram index is currently shown in 1D

◆ getPainter2D()

virtual std::unique_ptr<Painter2DBase> getPainter2D ( ) const

pure virtual

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

Returns: A painter

Implemented in LayerDataPeak, LayerDataIonMobility, LayerDataIdent, LayerDataFeature, LayerDataConsensus, and LayerDataChrom.

◆ getProjection()

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

pure virtual

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.

Implemented in LayerDataFeature, LayerDataConsensus, LayerDataPeak, LayerDataIonMobility, LayerDataIdent, and LayerDataChrom.

◆ getRange()

virtual RangeAllType getRange ( ) const

pure virtual

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()'

Implemented in LayerDataPeak, LayerDataIonMobility, LayerDataIdent, LayerDataFeature, LayerDataConsensus, LayerDataChrom, LayerData1DIonMobility, and LayerData1DChrom.

◆ getStats()

virtual std::unique_ptr<LayerStatistics> getStats ( ) const

pure virtual

Compute layer statistics (via visitor)

Implemented in LayerDataPeak, LayerDataIonMobility, LayerDataIdent, LayerDataFeature, LayerDataConsensus, and LayerDataChrom.

◆ operator=() [1/2]

LayerDataBase& operator= ( const LayerDataBase & ld )

delete

Assignment operator.

◆ operator=() [2/2]

LayerDataBase& operator= ( LayerDataBase && ld )

delete

Move assignment – deleted, by same argument as for move c'tor.

◆ peakIndexToXY()

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

pure virtual

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)

Implemented in LayerDataPeak, LayerDataIonMobility, LayerDataIdent, LayerDataFeature, LayerDataConsensus, and LayerDataChrom.

◆ setName()

void setName ( const String & new_name )

inline

Set the name of the layer, usually the basename of the file.

◆ setNameSuffix()

void setNameSuffix ( const String & decorator )

inline

set an extra annotation as suffix to the layers name, e.g. '[39]' for which chromatogram index is currently shown in 1D

◆ storeFullData()

virtual std::unique_ptr<LayerStoreData> storeFullData ( ) const

inlinevirtual

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 in LayerDataPeak, LayerDataIonMobility, LayerDataIdent, LayerDataFeature, LayerDataConsensus, LayerDataChrom, LayerData1DPeak, LayerData1DIonMobility, and LayerData1DChrom.

Referenced by TOPPViewBase::runTOPPTool_().

◆ storeVisibleData()

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

inlinevirtual

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

Reimplemented in LayerDataPeak, LayerDataIonMobility, LayerDataIdent, LayerDataFeature, LayerDataConsensus, LayerDataChrom, LayerData1DPeak, LayerData1DIonMobility, and LayerData1DChrom.

Referenced by TOPPViewBase::runTOPPTool_().

◆ to1DLayer()

virtual std::unique_ptr<LayerData1DBase> to1DLayer ( ) const

pure virtual

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

Implemented in LayerDataPeak, LayerDataIonMobility, LayerDataIdent, LayerDataFeature, LayerDataConsensus, and LayerDataChrom.

◆ updateRanges()

virtual void updateRanges ( )

pure virtual

Update ranges of the underlying data.

Implemented in LayerDataPeak, LayerDataIonMobility, LayerDataIdent, LayerDataFeature, LayerDataConsensus, LayerDataChrom, LayerData1DPeak, LayerData1DIonMobility, and LayerData1DChrom.

Member Data Documentation

◆ filename

String filename

file name of the file the data comes from (if available)

Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::fileChanged_(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), and TOPPViewBase::showCurrentPeaksAsIonMobility().

◆ filters

DataFilters filters

Filters to apply before painting.

Referenced by TOPPViewBase::runTOPPTool_().

◆ flags

std::bitset<SIZE_OF_FLAGS> flags

Actual state of each flag.

◆ gradient

MultiGradient gradient

Gradient for 2D and 3D views.

◆ label

LabelType label = L_NONE

Label type.

Referenced by TOPPViewBase::updateToolBar().

◆ modifiable

bool modifiable = false

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

◆ modified

bool modified = false

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

◆ name_

String name_

private

layer name

◆ name_suffix_

String name_suffix_

private

an extra annotation as suffix to the layers name, e.g. '[39]' for which chromatogram index is currently shown in 1D

◆ param

Param param

Layer parameters.

Referenced by TOPPViewBase::loadFiles().

◆ peptide_hit_index

int peptide_hit_index = -1

◆ peptide_id_index

int peptide_id_index = -1

Selected peptide id and hit index (-1 if none is selected)

◆ type

DataType type = DT_UNKNOWN

data type (peak or feature data, etc)

Referenced by TOPPViewBase::addData(), TOPPViewBase::copyLayer(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::updateMenu(), TOPPViewBase::updateToolBar(), and TOPPViewBase::zoomOtherWindows().

◆ visible

bool visible = true

if this layer is visible

Referenced by TOPPViewBase::editMetadata(), TOPPViewBase::rerunTOPPTool(), and TOPPViewBase::showTOPPDialog_().

Public Types

Public Member Functions

Public Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ RangeAllType

Constructor & Destructor Documentation

◆ LayerDataBase() [1/4]

◆ LayerDataBase() [2/4]

◆ LayerDataBase() [3/4]

◆ LayerDataBase() [4/4]

◆ ~LayerDataBase()

Member Function Documentation

◆ annotate()

◆ findClosestDataPoint()

◆ findHighestDataPoint()

◆ getDataArrayDescription()

◆ getDecoratedName()

◆ getMaxIntensity()

◆ getMinIntensity()

◆ getName()

◆ getNameSuffix()

◆ getPainter2D()

◆ getProjection()

◆ getRange()

◆ getStats()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ peakIndexToXY()

◆ setName()

◆ setNameSuffix()

◆ storeFullData()

◆ storeVisibleData()

◆ to1DLayer()

◆ updateRanges()

Member Data Documentation

◆ filename

◆ filters

◆ flags

◆ gradient

◆ label

◆ modifiable

◆ modified

◆ name_

◆ name_suffix_

◆ param

◆ peptide_hit_index

◆ peptide_id_index

◆ type

◆ visible