Base class for all 1D layers, a special case of LayerData. More...

#include <OpenMS/VISUAL/LayerData1DBase.h>

Inheritance diagram for LayerData1DBase:

Collaboration diagram for LayerData1DBase:

Public Member Functions
virtual std::unique_ptr< Painter1DBase >	getPainter1D () const =0
	Obtain a painter which can draw the layer on a canvas.

virtual RangeAllType	getRange1D () const =0

virtual RangeAllType	getRangeForArea (const RangeAllType partial_range) const =0
	Given a `partial_range` for the current 1D layer (e.g. an m/z range), fill in the other dimensions (usually intensity) from all data points which are within the input range.

virtual QMenu *	getContextMenuAnnotation (Annotation1DItem *annot_item, bool &need_repaint)=0
	Get a context menu (with lambda actions included) for this 1D layer, when a Annotation1DItem was right-clicked.

virtual Annotation1DItem *	addPeakAnnotation (const PeakIndex &peak_index, const QString &text, const QColor &color)=0
	Add a Annotation1DPeakItem to getCurrentAnnotations(). The specific type is determined by the derived class (e.g. Peak1D, ChromatogramPeak1D, etc)

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

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

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

const Annotations1DContainer &	getAnnotations (Size spectrum_index) const
	Returns a const reference to the annotations of the `spectrum_index's` spectrum (1D view)

Annotations1DContainer &	getAnnotations (Size spectrum_index)
	Returns a mutable reference to the annotations of the `spectrum_index's` spectrum (1D view)

Size	getCurrentIndex () const
	Get the index of the current spectrum (1D view)

void	setCurrentIndex (Size index)
	Set the index of the current spectrum (1D view) – and prepares annotations.

virtual bool	hasIndex (Size index) const =0
	Does the layer have at least `index` items (e.g. spectra, chroms, etc), so a call to setCurrentIndex() is valid?

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

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

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

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

	LayerDataBase (LayerDataBase &&ld)=delete

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

virtual	~LayerDataBase ()=default
	D'tor.

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

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)

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.

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)

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

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

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

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

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

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

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

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

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

virtual RangeAllType	getRange () const =0

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

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

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

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

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

Public Attributes
bool	flipped = false
	if this layer is flipped (1d mirror view)

std::vector< QColor >	peak_colors_1d
	Peak colors of the currently shown spectrum.

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

bool	visible = true
	if this layer is visible

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

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

Param	param
	Layer parameters.

MultiGradient	gradient
	Gradient for 2D and 3D views.

DataFilters	filters
	Filters to apply before painting.

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

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

LabelType	label = L_NONE
	Label type.

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

int	peptide_hit_index = -1

Protected Attributes
Size	current_idx_ = 0
	Index of the current spectrum/chromatogram etc (by default, show the first one)

std::vector< Annotations1DContainer >	annotations_1d_ = std::vector<Annotations1DContainer>(1)
	Annotations of all spectra of the experiment (1D view)

Additional Inherited Members
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.

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

typedef ConsensusMap	ConsensusMapType
	consensus features

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

typedef AnnotatedMSRun	ExperimentType
	Main data type (experiment)

typedef std::shared_ptr< ExperimentType >	ExperimentSharedPtrType
	SharedPtr on MSExperiment.

typedef std::shared_ptr< const ExperimentType >	ConstExperimentSharedPtrType

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

typedef std::shared_ptr< OSWData >	OSWDataSharedPtrType
	SharedPtr on OSWData.

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

Detailed Description

Base class for all 1D layers, a special case of LayerData.

1D is a bit special because we need to remember which spectrum/chrom/IM is currently shown (there are usually many of them to choose from).

Member Function Documentation

◆ addPeakAnnotation()

virtual Annotation1DItem * addPeakAnnotation	(	const PeakIndex &	peak_index,
		const QString &	text,
		const QColor &	color
	)

pure virtual

Add a Annotation1DPeakItem to getCurrentAnnotations(). The specific type is determined by the derived class (e.g. Peak1D, ChromatogramPeak1D, etc)

Parameters

peak_index	Which peak should be annotated?
text	Text to annotate with
color	Color of the text

Returns: The item that was created

Implemented in LayerData1DChrom, LayerData1DIonMobility, and LayerData1DPeak.

◆ getAnnotations() [1/2]

Annotations1DContainer & getAnnotations ( Size spectrum_index )

inline

Returns a mutable reference to the annotations of the spectrum_index's spectrum (1D view)

◆ getAnnotations() [2/2]

const Annotations1DContainer & getAnnotations ( Size spectrum_index ) const

inline

Returns a const reference to the annotations of the spectrum_index's spectrum (1D view)

◆ getContextMenuAnnotation()

virtual QMenu * getContextMenuAnnotation	(	Annotation1DItem *	annot_item,
		bool &	need_repaint
	)

pure virtual

Get a context menu (with lambda actions included) for this 1D layer, when a Annotation1DItem was right-clicked.

Parameters

annot_item	The annotation item clicked on
need_repaint	Reference of bool in calling function, which must know if the action requires repainting the canvas

Returns: A context menu to embed into the generic menu

Implemented in LayerData1DChrom, LayerData1DIonMobility, and LayerData1DPeak.

◆ getCurrentAnnotations() [1/2]

Annotations1DContainer & getCurrentAnnotations ( )

inline

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

◆ getCurrentAnnotations() [2/2]

const Annotations1DContainer & getCurrentAnnotations ( ) const

inline

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

◆ getCurrentIndex()

Size getCurrentIndex ( ) const

inline

Get the index of the current spectrum (1D view)

◆ getDecoratedName()

String getDecoratedName ( ) const

overridevirtual

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

Reimplemented from LayerDataBase.

◆ getPainter1D()

virtual std::unique_ptr< Painter1DBase > getPainter1D ( ) const

pure virtual

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

Returns: A painter

Implemented in LayerData1DChrom, LayerData1DIonMobility, and LayerData1DPeak.

◆ getRange1D()

virtual RangeAllType getRange1D ( ) const

pure virtual

Returns the data range in all known dimensions for the data of the currently active index (i.e. only a single spec/chrom/etc). 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 the whole layer (i.e. all specs/chroms/etc), call 'LayerDataBase::getRange()'

Implemented in LayerData1DChrom, LayerData1DIonMobility, and LayerData1DPeak.

◆ getRangeForArea()

virtual RangeAllType getRangeForArea ( const RangeAllType partial_range ) const

pure virtual

Given a partial_range for the current 1D layer (e.g. an m/z range), fill in the other dimensions (usually intensity) from all data points which are within the input range.

Parameters

partial_range Range with at least one dimension populated (which is used to filter the current spectrum/chrom/...)

Returns: Range of the data points within the input range (e.g. for spectra: m/z and intensity; or chroms: RT and intensity, etc)

Implemented in LayerData1DChrom, LayerData1DIonMobility, and LayerData1DPeak.

◆ hasIndex()

virtual bool hasIndex ( Size index ) const

pure virtual

Does the layer have at least index items (e.g. spectra, chroms, etc), so a call to setCurrentIndex() is valid?

Implemented in LayerData1DChrom, LayerData1DIonMobility, and LayerData1DPeak.

◆ setCurrentIndex()

void setCurrentIndex ( Size index )

Set the index of the current spectrum (1D view) – and prepares annotations.

Member Data Documentation

◆ annotations_1d_

std::vector<Annotations1DContainer> annotations_1d_ = std::vector<Annotations1DContainer>(1)

protected

Annotations of all spectra of the experiment (1D view)

◆ current_idx_

Size current_idx_ = 0

protected

Index of the current spectrum/chromatogram etc (by default, show the first one)

◆ flipped

bool flipped = false

if this layer is flipped (1d mirror view)

◆ peak_colors_1d

std::vector<QColor> peak_colors_1d

Peak colors of the currently shown spectrum.

Public Member Functions

Public Attributes

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ addPeakAnnotation()

◆ getAnnotations() [1/2]

◆ getAnnotations() [2/2]

◆ getContextMenuAnnotation()

◆ getCurrentAnnotations() [1/2]

◆ getCurrentAnnotations() [2/2]

◆ getCurrentIndex()

◆ getDecoratedName()

◆ getPainter1D()

◆ getRange1D()

◆ getRangeForArea()

◆ hasIndex()

◆ setCurrentIndex()

Member Data Documentation

◆ annotations_1d_

◆ current_idx_

◆ flipped

◆ peak_colors_1d