Base class for visualization canvas classes. More...

#include <OpenMS/VISUAL/PlotCanvas.h>

Inheritance diagram for PlotCanvas:

Collaboration diagram for PlotCanvas:

Protected Member Functions
reimplemented QT events
void	resizeEvent (QResizeEvent *e) override

void	wheelEvent (QWheelEvent *e) override

void	keyPressEvent (QKeyEvent *e) override

void	keyReleaseEvent (QKeyEvent *e) override

void	focusOutEvent (QFocusEvent *e) override

void	leaveEvent (QEvent *e) override

void	enterEvent (QEnterEvent *e) override

virtual void	intensityModeChange_ ()
	This method is called whenever the intensity mode changes. Reimplement if you need to react on such changes. More...

void	dimensionsChanged_ ()
	Call this whenever the DimMapper receives new dimensions; will update the axes and scrollbars. More...

virtual void	changeVisibleArea_ (VisibleArea new_area, bool repaint=true, bool add_to_stack=false)
	Sets the visible area. More...

virtual void	recalculateSnapFactor_ ()
	Recalculates the intensity scaling factor for 'snap to maximum intensity mode'. More...

Zoom stack methods
virtual void	zoom_ (int x, int y, bool zoom_in)
	Zooms such that screen point x, y would still point to the same data point. More...

void	zoomBack_ ()
	Go backward in zoom history. More...

virtual void	zoomForward_ ()
	Go forward in zoom history. More...

void	zoomAdd_ (const VisibleArea &area)
	Add a visible area to the zoom stack. More...

void	zoomClear_ ()
	Clears the zoom stack and invalidates the current zoom position. After calling this, a valid zoom position has to be added immediately. More...

Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Type definitions
enum	ActionModes { AM_TRANSLATE , AM_ZOOM , AM_MEASURE }
	Mouse action modes. More...

enum	IntensityModes { IM_NONE , IM_PERCENTAGE , IM_SNAP , IM_LOG }
	Display modes of intensity. More...

typedef LayerDataBase::ExperimentType	ExperimentType
	Main data type (experiment) More...

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

typedef LayerDataBase::ConstExperimentSharedPtrType	ConstExperimentSharedPtrType

typedef LayerDataBase::ODExperimentSharedPtrType	ODExperimentSharedPtrType

typedef LayerDataBase::FeatureMapType	FeatureMapType
	Main data type (features) More...

typedef LayerDataBase::FeatureMapSharedPtrType	FeatureMapSharedPtrType
	Main managed data type (features) More...

typedef LayerDataBase::ConsensusMapType	ConsensusMapType
	Main data type (consensus features) More...

typedef LayerDataBase::ConsensusMapSharedPtrType	ConsensusMapSharedPtrType
	Main managed data type (consensus features) More...

typedef ExperimentType::SpectrumType	SpectrumType
	Spectrum type. More...

typedef SpectrumType::ConstIterator	SpectrumConstIteratorType
	Spectrum iterator type (iterates over peaks) More...

typedef SpectrumType::PeakType	PeakType
	Peak type. More...

using	RangeType = RangeAllType
	a generic range for the most common units More...

using	AreaXYType = Area< 2 >::AreaXYType
	The range of data shown on the X and Y axis (unit depends on runtime config) More...

using	VisibleArea = Area< 2 >
	The visible range of data on X and Y axis as shown on plot axis (not necessarily the range of actual data, e.g. no data to show). More...

using	GenericArea = Area< 2 >
	A generic range of data on X and Y axis as shown on plot axis. More...

using	PixelArea = Area< 2 >

using	UnitRange = RangeAllType

using	PointOnAxis = DimMapper< 2 >::Point

	PlotCanvas (const Param &preferences, QWidget *parent=nullptr)
	Default constructor. More...

	~PlotCanvas () override
	Destructor. More...

void	setPlotWidget (PlotWidget *widget)
	Sets the spectrum widget. More...

PlotWidget *	getPlotWidget () const
	Returns the spectrum widget. More...

Int	getActionMode () const
	Returns the action mode. More...

IntensityModes	getIntensityMode () const
	Returns the intensity mode. More...

void	setIntensityMode (IntensityModes mod)
	Sets the intensity mode. More...

bool	gridLinesShown () const
	Returns if the grid is currently shown. More...

const LayerDataBase &	getLayer (Size index) const
	returns the layer data with index `index` More...

LayerDataBase &	getLayer (Size index)
	returns the layer data with index `index` More...

const LayerDataBase &	getCurrentLayer () const
	returns the layer data of the active layer More...

LayerDataBase &	getCurrentLayer ()
	returns the layer data of the active layer More...

Size	getCurrentLayerIndex () const
	returns the index of the active layer More...

bool	getLayerFlag (LayerDataBase::Flags f) const
	returns a layer flag of the current layer More...

void	setLayerFlag (LayerDataBase::Flags f, bool value)
	sets a layer flag of the current layer More...

bool	getLayerFlag (Size layer, LayerDataBase::Flags f) const
	returns a layer flag of the layer `layer` More...

void	setLayerFlag (Size layer, LayerDataBase::Flags f, bool value)
	sets a layer flag of the layer `layer` More...

void	setLabel (LayerDataBase::LabelType label)

const VisibleArea &	getVisibleArea () const
	Returns the currently visible area. This is the authority which determines the X and Y axis' scale. More...

bool	isVisible (const PointOnAxis &p) const

PixelArea	getPixelRange () const

virtual void	setFilters (const DataFilters &filters)
	Sets the filters applied to the data before drawing (for the current layer) More...

Translation methods, which are called when cursor buttons are pressed
QImage	buffer_
	Buffer that stores the actual peak information. More...

DimMapper< 2 >	unit_mapper_
	Mapper for X and Y axis. More...

ActionModes	action_mode_ = AM_TRANSLATE
	Stores the current action mode (Pick, Zoom, Translate) More...

IntensityModes	intensity_mode_ = IM_NONE
	Stores the used intensity mode function. More...

LayerStack	layers_
	Layer data. More...

VisibleArea	visible_area_
	Stores the currently visible area in data units (e.g. seconds, m/z, intensity etc) and axis (X,Y) area. More...

RangeType	overall_data_range_
	Stores the data range (m/z, RT and intensity) of all layers. More...

bool	show_grid_ = true
	Stores whether or not to show a grid. More...

std::vector< VisibleArea >	zoom_stack_
	The zoom stack. More...

std::vector< VisibleArea >::iterator	zoom_pos_ = zoom_stack_.end()
	The current position in the zoom stack. More...

bool	update_buffer_ = false
	Whether to recalculate the data in the buffer when repainting. More...

PlotWidget *	spectrum_widget_ = nullptr
	Back-pointer to the enclosing spectrum widget. More...

QPoint	last_mouse_pos_
	start position of mouse actions More...

double	percentage_factor_ = 1.0
	Intensity scaling factor for relative scale with multiple layers. More...

std::vector< double >	snap_factors_
	Intensity scaling factor for 'snap to maximum intensity mode'. More...

QRubberBand	rubber_band_
	Rubber band for selected area. More...

QMenu *	context_add_ = nullptr
	External context menu extension. More...

bool	show_timing_ = false
	Flag that determines if timing data is printed to the command line. More...

PeakIndex	selected_peak_
	selected peak More...

PeakIndex	measurement_start_
	start peak of measuring mode More...

virtual void	translateLeft_ (Qt::KeyboardModifiers m)
	Translation bound to the 'Left' key. More...

virtual void	translateRight_ (Qt::KeyboardModifiers m)
	Translation bound to the 'Right' key. More...

virtual void	translateForward_ ()
	Translation bound to the 'Up' key. More...

virtual void	translateBackward_ ()
	Translation bound to the 'Down' key. More...

virtual void	updateScrollbars_ ()
	Updates the scroll bars. More...

PointXYType	widgetToData_ (double x, double y)
	Convert widget (pixel) to chart (unit) coordinates. More...

PointXYType	widgetToData_ (const QPoint &pos)
	Calls widgetToData_ with x and y position of `pos`. More...

virtual void	paintGridLines_ (QPainter &painter)
	Helper function to paint grid lines. More...

virtual void	recalculateRanges_ ()
	Recalculates the overall_data_range_. More...

virtual void	update_ (const char *caller_name)
	Updates the displayed data. More...

void	modificationStatus_ (Size layer_index, bool modified)
	Takes all actions necessary when the modification status of a layer changes (signals etc.) More...

void	addDataProcessing_ (PeakMap &map, DataProcessing::ProcessingAction action) const
	Data processing setter for peak maps. More...

Dataset handling methods
See also changeVisibility
Size	getLayerCount () const
	Returns the number of layers. More...

virtual void	activateLayer (Size layer_index)=0
	change the active layer (the one that is used for selecting and so on) More...

virtual void	removeLayer (Size layer_index)=0
	removes the layer with index `layer_index` More...

void	removeLayers ()
	removes all layers by calling removeLayer() for all layer indices (from highest to lowest) More...

bool	addLayer (std::unique_ptr< LayerData1DBase > layer)
	Add an already constructed layer (e.g. for projections) More...

bool	addPeakLayer (const ExperimentSharedPtrType &map, ODExperimentSharedPtrType od_map, const String &filename="", const String &caption="", const bool use_noise_cutoff=false)
	Add a peak data layer. More...

bool	addChromLayer (const ExperimentSharedPtrType &map, ODExperimentSharedPtrType od_map, const String &filename="", const String &caption="")
	Add a chrom data layer. More...

bool	addLayer (FeatureMapSharedPtrType map, const String &filename="", const String &caption="")
	Add a feature data layer. More...

bool	addLayer (ConsensusMapSharedPtrType map, const String &filename="", const String &caption="")
	Add a consensus feature data layer. More...

bool	addLayer (std::vector< PeptideIdentification > &peptides, const String &filename="", const String &caption="")
	Add an identification data layer. More...

float	getCurrentMinIntensity () const
	Returns the minimum intensity of the active layer. More...

float	getCurrentMaxIntensity () const
	Returns the maximum intensity of the active layer. More...

float	getMinIntensity (Size index) const
	Returns the minimum intensity of the layer with index `index`. More...

float	getMaxIntensity (Size index) const
	Returns the maximum intensity of the layer with index `index`. More...

void	setLayerName (Size i, const String &name)
	Sets the `name` of layer `i`. More...

String	getLayerName (Size i)
	Gets the name of layer `i`. More...

void	setCurrentLayerParameters (const Param &param)
	Sets the parameters of the current layer. More...

virtual const RangeType &	getDataRange () const
	Returns the area which encloses all data points of all layers. More...

double	getSnapFactor ()
	Returns the first intensity scaling factor for 'snap to maximum intensity mode' (for the currently visible data range). More...

double	getPercentageFactor () const
	Returns the percentage factor. More...

virtual void	showCurrentLayerPreferences ()=0
	Shows the preferences dialog of the active layer. More...

virtual void	showMetaData (bool modifiable=false, Int index=-1)
	Shows a dialog with the meta data. More...

void	changeVisibility (Size i, bool b)
	change the visibility of a layer More...

void	changeLayerFilterState (Size i, bool b)
	change if the defined data filters are used More...

void	showGridLines (bool show)
	Whether or not to show grid lines. More...

virtual void	resetZoom (bool repaint=true)
	Zooms fully out and resets the zoom stack. More...

void	setVisibleArea (const VisibleArea &area)
	Sets the visible area. More...

void	setVisibleArea (const RangeAllType &area)
	Sets the visible area. More...

void	setVisibleArea (const AreaXYType &area)
	Sets the visible area. More...

void	setVisibleAreaX (double min, double max)
	Set only the visible area for the x axis; other axes are untouched. More...

void	setVisibleAreaY (double min, double max)
	Set only the visible area for the y axis; other axes are untouched. More...

void	saveCurrentLayer (bool visible)
	Saves the current layer data. More...

virtual void	horizontalScrollBarChange (int value)
	Notifies the canvas that the horizontal scrollbar has been moved. More...

virtual void	verticalScrollBarChange (int value)
	Notifies the canvas that the vertical scrollbar has been moved. More...

void	setAdditionalContextMenu (QMenu *menu)
	Sets the additional context menu. If not 0, this menu is added to the context menu of the canvas. More...

virtual void	updateLayer (Size i)=0
	Updates layer `i` when the data in the corresponding file changes. More...

AreaXYType	canvasPixelArea () const
	Get the Area in pixel coordinates of the current canvas for X and Y axis. More...

const DimMapper< 2 > &	getMapper () const
	Get Mapper to translate between values for axis (X/Y) and units (m/z, RT, intensity, ...) More...

void	setMapper (const DimMapper< 2 > &mapper)
	Set a new mapper for the canvas. More...

void	layerModficationChange (Size layer, bool modified)
	Signal emitted whenever the modification status of a layer changes (editing and storing) More...

void	layerActivated (QWidget *w)
	Signal emitted whenever a new layer is activated within the current window. More...

void	layerZoomChanged (QWidget *w)
	Signal emitted whenever the zoom changed. More...

void	visibleAreaChanged (const VisibleArea &area)
	Change of the visible area. More...

void	sendCursorStatus (const String &x_value, const String &y_value)
	Emitted when the cursor position changes (for displaying e.g. in status bar) More...

void	sendStatusMessage (std::string message, OpenMS::UInt time)
	Emits a status message that should be displayed for `time` ms. If `time` is 0 the message should be displayed until the next message is emitted. More...

void	recalculateAxes ()
	Forces recalculation of axis ticks in the connected widget. More...

void	updateVScrollbar (float f_min, float disp_min, float disp_max, float f_max)
	Triggers the update of the vertical scrollbar. More...

void	updateHScrollbar (float f_min, float disp_min, float disp_max, float f_max)
	Triggers the update of the horizontal scrollbar. More...

void	changeLegendVisibility ()
	Toggle axis legend visibility change. More...

void	actionModeChange ()
	Emitted when the action mode changes. More...

void	preferencesChange ()
	Emitted when the layer preferences have changed. More...

void	updateCursor_ ()
	Updates the cursor according to the current action mode. More...

void	drawText_ (QPainter &painter, const QStringList &text)
	Draws several lines of text to the upper right corner of the widget. More...

double	getIdentificationMZ_ (const Size layer_index, const PeptideIdentification &peptide) const
	Returns the m/z value of an identification depending on the m/z source of the layer (precursor mass/theoretical peptide mass) More...

virtual bool	finishAdding_ ()=0
	Method that is called when a new layer has been added. More...

void	popIncompleteLayer_ (const QString &error_message="")

Additional Inherited Members
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Detailed Description

Base class for visualization canvas classes.

This class is the base class for the spectrum data views which are used for 1D, 2D and 3D visualization of data. In TOPPView, each PlotCanvas is paired with an enclosing PlotWidget (see also the getPlotWidget() function that provides a back-reference). To provide additional spectrum views, you can derive from this class and you should also create a subclass from PlotWidget which encloses your class derived from PlotCanvas. A spectrum canvas can display multiple data layers at the same time (see layers_ member variable).

The actual data to be displayed is stored as a vector of LayerDataBase objects which hold the actual data. It also stores information about the commonly used constants such as ActionModes or IntensityModes.

All derived classes should follow these interface conventions:

Translate mode
- Activated by default
- Arrow keys can be used to translate without entering translate mode
Zoom mode
- Activated using the CTRL key
- Zoom stack traversal with CTRL+/CTRL- or mouses wheel
- Pressing the Backspace key resets the zoom (and stack)
Measure mode
- Activated using the SHIFT key

Member Typedef Documentation

◆ AreaXYType

using AreaXYType = Area<2>::AreaXYType

The range of data shown on the X and Y axis (unit depends on runtime config)

◆ ConsensusMapSharedPtrType

typedef LayerDataBase::ConsensusMapSharedPtrType ConsensusMapSharedPtrType

Main managed data type (consensus features)

◆ ConsensusMapType

typedef LayerDataBase::ConsensusMapType ConsensusMapType

Main data type (consensus features)

◆ ConstExperimentSharedPtrType

typedef LayerDataBase::ConstExperimentSharedPtrType ConstExperimentSharedPtrType

◆ ExperimentSharedPtrType

typedef LayerDataBase::ExperimentSharedPtrType ExperimentSharedPtrType

Main managed data type (experiment)

◆ ExperimentType

typedef LayerDataBase::ExperimentType ExperimentType

Main data type (experiment)

◆ FeatureMapSharedPtrType

typedef LayerDataBase::FeatureMapSharedPtrType FeatureMapSharedPtrType

Main managed data type (features)

◆ FeatureMapType

typedef LayerDataBase::FeatureMapType FeatureMapType

Main data type (features)

◆ GenericArea

using GenericArea = Area<2>

A generic range of data on X and Y axis as shown on plot axis.

◆ ODExperimentSharedPtrType

typedef LayerDataBase::ODExperimentSharedPtrType ODExperimentSharedPtrType

◆ PeakType

typedef SpectrumType::PeakType PeakType

Peak type.

◆ PixelArea

using PixelArea = Area<2>

The number of pixels on the axis. The lower point of the area will be zero. The maxima will reflect the number of pixels in either dimension. Note that the unit of the Axis etc is in PIXELS (-> not in seconds, m/z or whatever)

◆ PointOnAxis

using PointOnAxis = DimMapper<2>::Point

◆ RangeType

using RangeType = RangeAllType

a generic range for the most common units

◆ SpectrumConstIteratorType

typedef SpectrumType::ConstIterator SpectrumConstIteratorType

Spectrum iterator type (iterates over peaks)

◆ SpectrumType

typedef ExperimentType::SpectrumType SpectrumType

Spectrum type.

◆ UnitRange

using UnitRange = RangeAllType

◆ VisibleArea

using VisibleArea = Area<2>

The visible range of data on X and Y axis as shown on plot axis (not necessarily the range of actual data, e.g. no data to show).

Member Enumeration Documentation

◆ ActionModes

enum ActionModes

Mouse action modes.

Enumerator
AM_TRANSLATE	translate
AM_ZOOM	zoom
AM_MEASURE	measure

◆ IntensityModes

enum IntensityModes

Display modes of intensity.

Enumerator
IM_NONE	Normal mode: f(x)=x; y-axis shows the maximum of all layers, no scaling.
IM_PERCENTAGE	Shows intensities normalized by each layer's maximum: f(x)=x/max(x)*100.
IM_SNAP	Shows the maximum displayed intensity (across all layers) as if it was the overall maximum intensity.
IM_LOG	Logarithmic version of normal mode.

Constructor & Destructor Documentation

◆ PlotCanvas()

PlotCanvas	(	const Param &	preferences,
		QWidget *	parent = `nullptr`
	)

Default constructor.

◆ ~PlotCanvas()

~PlotCanvas ( )

override

Destructor.

Member Function Documentation

◆ actionModeChange

void actionModeChange ( )

signal

Emitted when the action mode changes.

◆ activateLayer()

virtual void activateLayer ( Size layer_index )

pure virtual

change the active layer (the one that is used for selecting and so on)

◆ addChromLayer()

bool addChromLayer	(	const ExperimentSharedPtrType &	map,
		ODExperimentSharedPtrType	od_map,
		const String &	filename = `""`,
		const String &	caption = `""`
	)

Add a chrom data layer.

Parameters

map	Shared pointer to input map. It can be performed in constant time and does not double the required memory.
od_map	Shared pointer to on disk data which potentially caches some data to save memory (the map can be empty, but do not pass nullptr).
filename	This absolute filename is used to monitor changes in the file and reload the data
caption	The caption of the layer (shown in the layer window)

Returns: If a new layer was created

Referenced by TOPPViewBase::addData().

◆ addDataProcessing_()

void addDataProcessing_	(	PeakMap &	map,
		DataProcessing::ProcessingAction	action
	)		const

inlineprotected

Data processing setter for peak maps.

References VersionInfo::getVersion(), DateTime::now(), and MSExperiment::size().

◆ addLayer() [1/4]

bool addLayer	(	ConsensusMapSharedPtrType	map,
		const String &	filename = `""`,
		const String &	caption = `""`
	)

Add a consensus feature data layer.

Parameters

map	Shared Pointer to input map. It can be performed in constant time and does not double the required memory.
filename	This absolute filename is used to monitor changes in the file and reload the data
caption	The caption of the layer (shown in the layer window)

Returns: If a new layer was created

◆ addLayer() [2/4]

bool addLayer	(	FeatureMapSharedPtrType	map,
		const String &	filename = `""`,
		const String &	caption = `""`
	)

Add a feature data layer.

Parameters

map	Shared Pointer to input map. It can be performed in constant time and does not double the required memory.
filename	This absolute filename is used to monitor changes in the file and reload the data
caption	The caption of the layer (shown in the layer window)

Returns: If a new layer was created

◆ addLayer() [3/4]

bool addLayer ( std::unique_ptr< LayerData1DBase > layer )

Add an already constructed layer (e.g. for projections)

Referenced by TOPPViewBase::addData().

◆ addLayer() [4/4]

bool addLayer	(	std::vector< PeptideIdentification > &	peptides,
		const String &	filename = `""`,
		const String &	caption = `""`
	)

Add an identification data layer.

Parameters

peptides	Input list of peptides, which has to be mutable and will be empty after adding. Swapping is used to insert the data. It can be performed in constant time and does not double the required memory.
filename	This absolute filename is used to monitor changes in the file and reload the data
caption	The caption of the layer (shown in the layer window)

Returns: If a new layer was created

◆ addPeakLayer()

bool addPeakLayer	(	const ExperimentSharedPtrType &	map,
		ODExperimentSharedPtrType	od_map,
		const String &	filename = `""`,
		const String &	caption = `""`,
		const bool	use_noise_cutoff = `false`
	)

Add a peak data layer.

Parameters

map	Shared pointer to input map. It can be performed in constant time and does not double the required memory.
od_map	Shared pointer to on disk data which potentially caches some data to save memory (the map can be empty, but do not pass nullptr).
filename	This absolute filename is used to monitor changes in the file and reload the data
caption	The caption of the layer (shown in the layer window)
use_noise_cutoff	Add a noise filter which removes low-intensity peaks

Returns: If a new layer was created

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

◆ canvasPixelArea

AreaXYType canvasPixelArea ( ) const

inlineslot

Get the Area in pixel coordinates of the current canvas for X and Y axis.

Returns

◆ changeLayerFilterState

void changeLayerFilterState	(	Size	i,
		bool	b
	)

slot

change if the defined data filters are used

Parameters

i	the index of the layer
b	true if layer is supposed to be visible

Referenced by TOPPViewBase::layerFilterVisibilityChange().

◆ changeLegendVisibility

void changeLegendVisibility ( )

signal

Toggle axis legend visibility change.

◆ changeVisibility

void changeVisibility	(	Size	i,
		bool	b
	)

slot

change the visibility of a layer

Parameters

i	the index of the layer
b	true if layer is supposed to be visible

◆ changeVisibleArea_()

virtual void changeVisibleArea_	(	VisibleArea	new_area,
		bool	repaint = `true`,
		bool	add_to_stack = `false`
	)

protectedvirtual

Sets the visible area.

Changes the visible area, adjusts the zoom stack and notifies interested clients about the change. If the area is outside the overall data range, the new area is pushed back into the overall range.

Parameters

new_area	The new visible area.
repaint	If true, a complete repaint is forced.
add_to_stack	If true the new area is to add to the zoom_stack_.

Reimplemented in Plot1DCanvas.

Referenced by Plot1DCanvas::resetZoom().

◆ dimensionsChanged_()

void dimensionsChanged_ ( )

protected

Call this whenever the DimMapper receives new dimensions; will update the axes and scrollbars.

◆ drawText_()

void drawText_	(	QPainter &	painter,
		const QStringList &	text
	)

protected

Draws several lines of text to the upper right corner of the widget.

◆ enterEvent()

void enterEvent ( QEnterEvent * e )

overrideprotected

◆ finishAdding_()

virtual bool finishAdding_ ( )

protectedpure virtual

Method that is called when a new layer has been added.

Implemented in Plot3DCanvas, Plot2DCanvas, and Plot1DCanvas.

◆ focusOutEvent()

void focusOutEvent ( QFocusEvent * e )

overrideprotected

◆ getActionMode()

Int getActionMode ( ) const

inline

Returns the action mode.

Returns the current action mode of type ActionModes

Returns: the current action mode

◆ getCurrentLayer() [1/2]

LayerDataBase& getCurrentLayer ( )

inline

returns the layer data of the active layer

◆ getCurrentLayer() [2/2]

const LayerDataBase& getCurrentLayer ( ) const

inline

returns the layer data of the active layer

Referenced by TOPPViewBase::annotateWithAMS(), TOPPViewBase::annotateWithID(), TOPPViewBase::annotateWithOSW(), TOPPViewBase::copyLayer(), TOPPViewBase::editMetadata(), TOPPViewBase::getCurrentLayer(), TOPPViewBase::loadFiles(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), TOPPViewBase::showPlotWidgetInWindow(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::updateToolBar(), and TOPPViewBase::zoomOtherWindows().

◆ getCurrentLayerIndex()

Size getCurrentLayerIndex ( ) const

inline

returns the index of the active layer

Referenced by TOPPViewBase::showCurrentPeaksAs3D(), and TOPPViewBase::showCurrentPeaksAsDIA().

◆ getCurrentMaxIntensity()

float getCurrentMaxIntensity ( ) const

inline

Returns the maximum intensity of the active layer.

◆ getCurrentMinIntensity()

float getCurrentMinIntensity ( ) const

inline

Returns the minimum intensity of the active layer.

◆ getDataRange()

virtual const RangeType& getDataRange ( ) const

virtual

Returns the area which encloses all data points of all layers.

See also: overall_data_range_

Reimplemented in Plot1DCanvas.

◆ getIdentificationMZ_()

double getIdentificationMZ_	(	const Size	layer_index,
		const PeptideIdentification &	peptide
	)		const

protected

Returns the m/z value of an identification depending on the m/z source of the layer (precursor mass/theoretical peptide mass)

◆ getIntensityMode()

IntensityModes getIntensityMode ( ) const

inline

Returns the intensity mode.

Returns the current intensity mode of type IntensityModes

Returns: the current intensity mode

Referenced by TOPPViewBase::updateToolBar().

◆ getLayer() [1/2]

LayerDataBase& getLayer ( Size index )

inline

returns the layer data with index index

◆ getLayer() [2/2]

const LayerDataBase& getLayer ( Size index ) const

inline

returns the layer data with index index

Referenced by TOPPViewBase::addData(), TOPPViewBase::fileChanged_(), and TOPPViewBase::showCurrentPeaksAs3D().

◆ getLayerCount()

Size getLayerCount ( ) const

inline

Returns the number of layers.

Referenced by TOPPViewBase::addData(), TOPPViewBase::fileChanged_(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::updateFilterBar(), and TOPPViewBase::updateToolBar().

◆ getLayerFlag() [1/2]

bool getLayerFlag ( LayerDataBase::Flags f ) const

inline

returns a layer flag of the current layer

Referenced by TOPPViewBase::changeUnassigned(), and TOPPViewBase::updateToolBar().

◆ getLayerFlag() [2/2]

bool getLayerFlag	(	Size	layer,
		LayerDataBase::Flags	f
	)		const

inline

returns a layer flag of the layer layer

◆ getLayerName()

String getLayerName ( Size i )

Gets the name of layer i.

Referenced by TOPPViewBase::addData().

◆ getMapper

const DimMapper<2>& getMapper ( ) const

slot

Get Mapper to translate between values for axis (X/Y) and units (m/z, RT, intensity, ...)

Returns: The translation from axis to units

Referenced by Annotation1DCaret< DataPoint >::draw(), and Annotation1DPeakItem< DataPoint >::draw().

◆ getMaxIntensity()

float getMaxIntensity ( Size index ) const

inline

Returns the maximum intensity of the layer with index index.

◆ getMinIntensity()

float getMinIntensity ( Size index ) const

inline

Returns the minimum intensity of the layer with index index.

◆ getPercentageFactor()

double getPercentageFactor ( ) const

Returns the percentage factor.

◆ getPixelRange()

PixelArea getPixelRange ( ) const

inline

Get the number of pixels of the current canvas (this is independent of the current visible area and zoom level). It's just the size of the canvas.

References Area< N_DIM >::setArea().

◆ getPlotWidget()

PlotWidget* getPlotWidget ( ) const

inline

Returns the spectrum widget.

Returns the enclosing spectrum widget

Returns: the spectrum widget

◆ getSnapFactor()

double getSnapFactor ( )

Returns the first intensity scaling factor for 'snap to maximum intensity mode' (for the currently visible data range).

See also: snap_factors_

◆ getVisibleArea()

const VisibleArea& getVisibleArea ( ) const

inline

Returns the currently visible area. This is the authority which determines the X and Y axis' scale.

See also: visible_area_

Referenced by TOPPViewBase::zoomOtherWindows().

◆ gridLinesShown()

bool gridLinesShown ( ) const

inline

Returns if the grid is currently shown.

Returns: true if the grid is visible, false otherwise

◆ horizontalScrollBarChange

virtual void horizontalScrollBarChange ( int value )

virtualslot

Notifies the canvas that the horizontal scrollbar has been moved.

Reimplement this slot to react on scrollbar events.

◆ intensityModeChange_()

virtual void intensityModeChange_ ( )

protectedvirtual

This method is called whenever the intensity mode changes. Reimplement if you need to react on such changes.

Reimplemented in Plot2DCanvas, and Plot1DCanvas.

◆ isVisible()

bool isVisible ( const PointOnAxis & p ) const

inline

Given a 2D axis coordinate, is it in the currently visible area? (useful to avoid plotting stuff outside the visible area) Note: The input p must have unit coordinates (i.e. the result of widgetToData_), not pixel coordinates.

◆ keyPressEvent()

void keyPressEvent ( QKeyEvent * e )

overrideprotected

◆ keyReleaseEvent()

void keyReleaseEvent ( QKeyEvent * e )

overrideprotected

◆ layerActivated

void layerActivated ( QWidget * w )

signal

Signal emitted whenever a new layer is activated within the current window.

Referenced by TOPPViewBase::showPlotWidgetInWindow().

◆ layerModficationChange

void layerModficationChange	(	Size	layer,
		bool	modified
	)

signal

Signal emitted whenever the modification status of a layer changes (editing and storing)

Referenced by TOPPViewBase::showPlotWidgetInWindow().

◆ layerZoomChanged

void layerZoomChanged ( QWidget * w )

signal

Signal emitted whenever the zoom changed.

Referenced by TOPPViewBase::showPlotWidgetInWindow().

◆ leaveEvent()

void leaveEvent ( QEvent * e )

overrideprotected

◆ modificationStatus_()

void modificationStatus_	(	Size	layer_index,
		bool	modified
	)

protected

Takes all actions necessary when the modification status of a layer changes (signals etc.)

◆ paintGridLines_()

virtual void paintGridLines_ ( QPainter & painter )

protectedvirtual

Helper function to paint grid lines.

Reimplemented in Plot1DCanvas.

◆ popIncompleteLayer_()

void popIncompleteLayer_ ( const QString & error_message = "" )

protected

remove already added layer which did not pass final checks in finishAdding_()

Parameters

error_message Optional error message to show as messagebox

◆ preferencesChange

void preferencesChange ( )

signal

Emitted when the layer preferences have changed.

Referenced by TOPPViewBase::showPlotWidgetInWindow().

◆ recalculateAxes

void recalculateAxes ( )

signal

Forces recalculation of axis ticks in the connected widget.

◆ recalculateRanges_()

virtual void recalculateRanges_ ( )

protectedvirtual

Recalculates the overall_data_range_.

A small margin is added to each side of the range in order to display all data.

Reimplemented in Plot1DCanvas.

Referenced by Plot1DCanvas::recalculateRanges_().

◆ recalculateSnapFactor_()

virtual void recalculateSnapFactor_ ( )

protectedvirtual

Recalculates the intensity scaling factor for 'snap to maximum intensity mode'.

See also: snap_factors_

Reimplemented in Plot2DCanvas.

◆ removeLayer()

virtual void removeLayer ( Size layer_index )

pure virtual

removes the layer with index layer_index

◆ removeLayers()

void removeLayers ( )

inline

removes all layers by calling removeLayer() for all layer indices (from highest to lowest)

◆ resetZoom

virtual void resetZoom ( bool repaint = true )

virtualslot

Zooms fully out and resets the zoom stack.

Sets the visible area to the initial value, such that all data is shown.

Parameters

repaint If true a repaint is forced. Otherwise only the new area is set.

Reimplemented in Plot1DCanvas.

Referenced by TOPPViewBase::resetZoom().

◆ resizeEvent()

void resizeEvent ( QResizeEvent * e )

overrideprotected

◆ saveCurrentLayer

void saveCurrentLayer ( bool visible )

slot

Saves the current layer data.

Parameters

visible If true, only the visible data is stored. Otherwise the whole data is stored.

Referenced by TOPPViewBase::saveLayerAll(), and TOPPViewBase::saveLayerVisible().

◆ sendCursorStatus

void sendCursorStatus	(	const String &	x_value,
		const String &	y_value
	)

signal

Emitted when the cursor position changes (for displaying e.g. in status bar)

◆ sendStatusMessage

void sendStatusMessage	(	std::string	message,
		OpenMS::UInt	time
	)

signal

Emits a status message that should be displayed for time ms. If time is 0 the message should be displayed until the next message is emitted.

◆ setAdditionalContextMenu

void setAdditionalContextMenu ( QMenu * menu )

slot

Sets the additional context menu. If not 0, this menu is added to the context menu of the canvas.

◆ setCurrentLayerParameters()

void setCurrentLayerParameters ( const Param & param )

inline

Sets the parameters of the current layer.

Referenced by TOPPViewBase::loadFiles().

◆ setFilters()

virtual void setFilters ( const DataFilters & filters )

virtual

Sets the filters applied to the data before drawing (for the current layer)

Referenced by TOPPViewBase::TOPPViewBase().

◆ setIntensityMode()

void setIntensityMode ( IntensityModes mod )

inline

Sets the intensity mode.

Sets the intensity mode and calls intensityModeChange_()

Parameters

mod	the new intensity mode

See also: intensityModeChange_()

◆ setLabel()

void setLabel ( LayerDataBase::LabelType label )

inline

Referenced by TOPPViewBase::changeLabel().

◆ setLayerFlag() [1/2]

void setLayerFlag	(	LayerDataBase::Flags	f,
		bool	value
	)

inline

sets a layer flag of the current layer

Referenced by TOPPViewBase::changeUnassigned().

◆ setLayerFlag() [2/2]

void setLayerFlag	(	Size	layer,
		LayerDataBase::Flags	f,
		bool	value
	)

inline

sets a layer flag of the layer layer

◆ setLayerName()

void setLayerName	(	Size	i,
		const String &	name
	)

Sets the name of layer i.

Referenced by TOPPViewBase::addData(), and TOPPViewBase::showCurrentPeaksAsDIA().

◆ setMapper

void setMapper ( const DimMapper< 2 > & mapper )

slot

Set a new mapper for the canvas.

Parameters

mapper The new mapper for translating between units and axis

◆ setPlotWidget()

void setPlotWidget ( PlotWidget * widget )

inline

Sets the spectrum widget.

Sets the enclosing spectrum widget. Call this from your PlotWidget derived class.

Parameters

widget the spectrum widget

◆ setVisibleArea [1/3]

void setVisibleArea ( const AreaXYType & area )

slot

Sets the visible area.

Sets the visible area to a new value and emits visibleAreaChanged() if the area is different from the old one.

Parameters

area	the new visible area

◆ setVisibleArea [2/3]

void setVisibleArea ( const RangeAllType & area )

slot

Sets the visible area.

Sets the visible area to a new value and emits visibleAreaChanged() if the area is different from the old one.

Parameters

area	the new visible area

◆ setVisibleArea [3/3]

void setVisibleArea ( const VisibleArea & area )

slot

Sets the visible area.

Sets the visible area to a new value and emits visibleAreaChanged() if the area is different from the old one.

Parameters

area	the new visible area

Referenced by TOPPViewBase::showCurrentPeaksAs3D(), and TOPPViewBase::zoomOtherWindows().

◆ setVisibleAreaX

void setVisibleAreaX	(	double	min,
		double	max
	)

slot

Set only the visible area for the x axis; other axes are untouched.

Parameters

min
max

◆ setVisibleAreaY

void setVisibleAreaY	(	double	min,
		double	max
	)

slot

Set only the visible area for the y axis; other axes are untouched.

Parameters

min
max

◆ showCurrentLayerPreferences()

virtual void showCurrentLayerPreferences ( )

pure virtual

Shows the preferences dialog of the active layer.

Implemented in Plot3DCanvas, Plot2DCanvas, and Plot1DCanvas.

Referenced by TOPPViewBase::showPreferences().

◆ showGridLines

void showGridLines ( bool show )

slot

Whether or not to show grid lines.

Sets whether grid lines are shown or not.

Parameters

show	Boolean variable deciding whether or not to show the grid lines.

Referenced by TOPPViewBase::toggleGridLines().

◆ showMetaData()

virtual void showMetaData	(	bool	modifiable = `false`,
		Int	index = `-1`
	)

virtual

Shows a dialog with the meta data.

Parameters

modifiable	indicates if the data can be modified.
index	If given, the meta data of the corresponding element (spectrum, feature, consensus feature) is shown instead of the layer meta data.

Referenced by TOPPViewBase::editMetadata(), and TOPPViewBase::showSpectrumMetaData().

◆ translateBackward_()

virtual void translateBackward_ ( )

protectedvirtual

Translation bound to the 'Down' key.

Reimplemented in Plot2DCanvas, and Plot1DCanvas.

◆ translateForward_()

virtual void translateForward_ ( )

protectedvirtual

Translation bound to the 'Up' key.

Reimplemented in Plot2DCanvas, and Plot1DCanvas.

◆ translateLeft_()

virtual void translateLeft_ ( Qt::KeyboardModifiers m )

protectedvirtual

Translation bound to the 'Left' key.

Reimplemented in Plot2DCanvas, and Plot1DCanvas.

◆ translateRight_()

virtual void translateRight_ ( Qt::KeyboardModifiers m )

protectedvirtual

Translation bound to the 'Right' key.

Reimplemented in Plot2DCanvas, and Plot1DCanvas.

◆ update_()

virtual void update_ ( const char * caller_name )

protectedvirtual

Updates the displayed data.

The default implementation calls QWidget::update().

This method is reimplemented in the 3D view to update the OpenGL widget.

Parameters

caller_name Name of the calling function (use OPENMS_PRETTY_FUNCTION).

Reimplemented in Plot3DCanvas.

◆ updateCursor_

void updateCursor_ ( )

protectedslot

Updates the cursor according to the current action mode.

◆ updateHScrollbar

void updateHScrollbar	(	float	f_min,
		float	disp_min,
		float	disp_max,
		float	f_max
	)

signal

Triggers the update of the horizontal scrollbar.

◆ updateLayer

virtual void updateLayer ( Size i )

pure virtualslot

Updates layer i when the data in the corresponding file changes.

Referenced by TOPPViewBase::fileChanged_().

◆ updateScrollbars_()

virtual void updateScrollbars_ ( )

protectedvirtual

Updates the scroll bars.

Updates the scrollbars after a change of the visible area.

Reimplemented in Plot2DCanvas, and Plot1DCanvas.

◆ updateVScrollbar

void updateVScrollbar	(	float	f_min,
		float	disp_min,
		float	disp_max,
		float	f_max
	)

signal

Triggers the update of the vertical scrollbar.

◆ verticalScrollBarChange

virtual void verticalScrollBarChange ( int value )

virtualslot

Notifies the canvas that the vertical scrollbar has been moved.

Reimplement this slot to react on scrollbar events.

◆ visibleAreaChanged

void visibleAreaChanged ( const VisibleArea & area )

signal

Change of the visible area.

Signal emitted whenever the visible area changes.

Parameters

area	The new visible area.

◆ wheelEvent()

void wheelEvent ( QWheelEvent * e )

overrideprotected

◆ widgetToData_() [1/2]

PointXYType widgetToData_ ( const QPoint & pos )

inlineprotected

Calls widgetToData_ with x and y position of pos.

◆ widgetToData_() [2/2]

PointXYType widgetToData_	(	double	x,
		double	y
	)

inlineprotected

Convert widget (pixel) to chart (unit) coordinates.

Translates widget coordinates to chart coordinates.

Parameters

x	the widget coordinate x
y	the widget coordinate y

Returns: chart coordinates

◆ zoom_()

virtual void zoom_	(	int	x,
		int	y,
		bool	zoom_in
	)

protectedvirtual

Zooms such that screen point x, y would still point to the same data point.

Reimplemented in Plot1DCanvas.

◆ zoomAdd_()

void zoomAdd_ ( const VisibleArea & area )

protected

Add a visible area to the zoom stack.

◆ zoomBack_()

void zoomBack_ ( )

protected

Go backward in zoom history.

◆ zoomClear_()

void zoomClear_ ( )

protected

Clears the zoom stack and invalidates the current zoom position. After calling this, a valid zoom position has to be added immediately.

◆ zoomForward_()

virtual void zoomForward_ ( )

protectedvirtual

Go forward in zoom history.

Reimplemented in Plot1DCanvas.

Member Data Documentation

◆ action_mode_

ActionModes action_mode_ = AM_TRANSLATE

protected

Stores the current action mode (Pick, Zoom, Translate)

◆ buffer_

QImage buffer_

protected

Buffer that stores the actual peak information.

◆ context_add_

QMenu* context_add_ = nullptr

protected

External context menu extension.

◆ intensity_mode_

IntensityModes intensity_mode_ = IM_NONE

protected

Stores the used intensity mode function.

◆ last_mouse_pos_

QPoint last_mouse_pos_

protected

start position of mouse actions

◆ layers_

LayerStack layers_

protected

Layer data.

◆ measurement_start_

PeakIndex measurement_start_

protected

start peak of measuring mode

◆ overall_data_range_

RangeType overall_data_range_

protected

Stores the data range (m/z, RT and intensity) of all layers.

◆ percentage_factor_

double percentage_factor_ = 1.0

protected

Intensity scaling factor for relative scale with multiple layers.

In this mode all layers are scaled to the same maximum. FIXME: this factor changes, depending on the layer which is currently plotted! Ouch!

◆ rubber_band_

QRubberBand rubber_band_

protected

Rubber band for selected area.

◆ selected_peak_

PeakIndex selected_peak_

protected

selected peak

◆ show_grid_

bool show_grid_ = true

protected

Stores whether or not to show a grid.

◆ show_timing_

bool show_timing_ = false

protected

Flag that determines if timing data is printed to the command line.

◆ snap_factors_

std::vector<double> snap_factors_

protected

Intensity scaling factor for 'snap to maximum intensity mode'.

In this mode the highest currently visible intensity is treated like the maximum overall intensity.

Only used in 2D mode.

◆ spectrum_widget_

PlotWidget* spectrum_widget_ = nullptr

protected

Back-pointer to the enclosing spectrum widget.

◆ unit_mapper_

DimMapper<2> unit_mapper_

protected

Mapper for X and Y axis.

◆ update_buffer_

bool update_buffer_ = false

protected

Whether to recalculate the data in the buffer when repainting.

◆ visible_area_

VisibleArea visible_area_

protected

Stores the currently visible area in data units (e.g. seconds, m/z, intensity etc) and axis (X,Y) area.

This is always (and only) the data shown in the widget. In 1D, the gravity axis may get some headroom on the y-axis, see Plot1DCanvas::correctGravityAxisOfVisibleArea_()

◆ zoom_pos_

std::vector<VisibleArea>::iterator zoom_pos_ = zoom_stack_.end()

protected

The current position in the zoom stack.

◆ zoom_stack_

std::vector<VisibleArea> zoom_stack_

protected

The zoom stack.

Protected Member Functions

Type definitions

Translation methods, which are called when cursor buttons are pressed

Dataset handling methods

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ AreaXYType

◆ ConsensusMapSharedPtrType

◆ ConsensusMapType

◆ ConstExperimentSharedPtrType

◆ ExperimentSharedPtrType

◆ ExperimentType

◆ FeatureMapSharedPtrType

◆ FeatureMapType

◆ GenericArea

◆ ODExperimentSharedPtrType

◆ PeakType

◆ PixelArea

◆ PointOnAxis

◆ RangeType

◆ SpectrumConstIteratorType

◆ SpectrumType

◆ UnitRange

◆ VisibleArea

Member Enumeration Documentation

◆ ActionModes

◆ IntensityModes

Constructor & Destructor Documentation

◆ PlotCanvas()

◆ ~PlotCanvas()

Member Function Documentation

◆ actionModeChange

◆ activateLayer()

◆ addChromLayer()

◆ addDataProcessing_()

◆ addLayer() [1/4]

◆ addLayer() [2/4]

◆ addLayer() [3/4]

◆ addLayer() [4/4]

◆ addPeakLayer()

◆ canvasPixelArea

◆ changeLayerFilterState

◆ changeLegendVisibility

◆ changeVisibility

◆ changeVisibleArea_()

◆ dimensionsChanged_()

◆ drawText_()

◆ enterEvent()

◆ finishAdding_()

◆ focusOutEvent()

◆ getActionMode()

◆ getCurrentLayer() [1/2]

◆ getCurrentLayer() [2/2]

◆ getCurrentLayerIndex()

◆ getCurrentMaxIntensity()

◆ getCurrentMinIntensity()

◆ getDataRange()

◆ getIdentificationMZ_()

◆ getIntensityMode()

◆ getLayer() [1/2]

◆ getLayer() [2/2]

◆ getLayerCount()

◆ getLayerFlag() [1/2]

◆ getLayerFlag() [2/2]

◆ getLayerName()

◆ getMapper

◆ getMaxIntensity()

◆ getMinIntensity()

◆ getPercentageFactor()

◆ getPixelRange()

◆ getPlotWidget()

◆ getSnapFactor()

◆ getVisibleArea()

◆ gridLinesShown()

◆ horizontalScrollBarChange

◆ intensityModeChange_()

◆ isVisible()

◆ keyPressEvent()

◆ keyReleaseEvent()