Canvas for 2D-visualization of peak map, feature map and consensus map data. More...

#include <OpenMS/VISUAL/Spectrum2DCanvas.h>

Inheritance diagram for Spectrum2DCanvas:

Collaboration diagram for Spectrum2DCanvas:

Public Slots
void	activateLayer (Size layer_index) override

void	removeLayer (Size layer_index) override

void	updateLayer (Size i) override

void	horizontalScrollBarChange (int value) override

void	verticalScrollBarChange (int value) override

void	updateProjections ()
	Updates the projection data and emits some related signals. More...

Public Slots inherited from SpectrumCanvas
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...

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

void	setVisibleArea (AreaType area)
	Sets the visible area. 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...

void	getVisiblePeakData (ExperimentType &map) const
	Fills the handed over `map` with the visible peaks of the current layer. More...

void	getVisibleFeatureData (FeatureMapType &map) const
	Fills the handed over `map` with the visible features of the current layer. More...

void	getVisibleConsensusData (ConsensusMapType &map) const
	Fills the handed over `map` with the visible consensus features of the current layer. More...

void	getVisibleIdentifications (std::vector< PeptideIdentification > &peptides) const
	Fills the handed over `peptides` with the visible peptide identifications of the current layer. More...

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

Signals
void	showProjectionHorizontal (ExperimentSharedPtrType)
	Sets the data for the horizontal projection. More...

void	showProjectionVertical (ExperimentSharedPtrType)
	Sets the data for the vertical projection. More...

void	showProjectionInfo (int, double, double)
	Shows the number of peaks and the intensity sum of the projection. More...

void	toggleProjections ()
	Signal emitted when the projections are to be shown/hidden. More...

void	showSpectrumAs1D (int index)
	Requests to display the spectrum with index `index` in 1D. More...

void	showSpectrumAs1D (std::vector< int, std::allocator< int > > indices)

void	showCurrentPeaksAs3D ()
	Requests to display all spectra in 3D plot. More...

Signals inherited from SpectrumCanvas
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 (DRange< 2 > area)
	Change of the visible area. More...

void	sendCursorStatus (double mz=-1.0, double rt=-1.0)
	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, float, float, float)
	Triggers the update of the vertical scrollbar. More...

void	updateHScrollbar (float, float, float, float)
	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...

Public Member Functions
	Spectrum2DCanvas (const Param &preferences, QWidget *parent=nullptr)
	Default constructor. More...

	~Spectrum2DCanvas () override
	Destructor. More...

void	showCurrentLayerPreferences () override
	Shows the preferences dialog of the active layer. More...

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

void	mergeIntoLayer (Size i, FeatureMapSharedPtrType map)
	Merges the features in `map` into the features layer `i`. More...

void	mergeIntoLayer (Size i, ConsensusMapSharedPtrType map)
	Merges the consensus features in `map` into the features layer `i`. More...

void	mergeIntoLayer (Size i, std::vector< PeptideIdentification > &peptides)
	Merges the peptide identifications in `peptides` into the peptide layer `i`. More...

void	recalculateCurrentLayerDotGradient ()
	recalculates the dot gradient of the active layer More...

Public Member Functions inherited from SpectrumCanvas
	SpectrumCanvas (const Param &preferences, QWidget *parent=nullptr)
	Default constructor. More...

	~SpectrumCanvas () override
	Destructor. More...

void	setSpectrumWidget (SpectrumWidget *widget)
	Sets the spectrum widget. More...

SpectrumWidget *	getSpectrumWidget () 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 LayerData &	getLayer (Size index) const
	returns the layer data with index `index` More...

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

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

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

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

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

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

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

void	setLabel (LayerData::LabelType label)

const AreaType &	getVisibleArea () const
	Returns the currently visible area. More...

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

bool	isMzToXAxis ()
	Returns the mapping of m/z to axes. More...

void	mzToXAxis (bool mz_to_x_axis)
	Sets the mapping of m/z to axes. More...

Size	getLayerCount () const
	Returns the number of layers. More...

Size	activeLayerIndex () const
	Returns the index of the active layer. 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...

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

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

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

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

const DRange< 3 > &	getDataRange ()
	Returns the area which encloses all data points. More...

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

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

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

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...

virtual 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...

Protected Slots
void	currentLayerParametersChanged_ ()
	Reacts on changed layer parameters. More...

Protected Slots inherited from SpectrumCanvas
void	updateCursor_ ()
	Updates the cursor according to the current action mode. More...

Protected Member Functions
bool	finishAdding_ () override
	Method that is called when a new layer has been added. More...

bool	collectFragmentScansInArea (double rt_min, double rt_max, double mz_min, double mz_max, QAction a, QMenu msn_scans, QMenu *msn_meta)
	Collects fragment ion scans in the indicated RT/mz area and adds them to the indicated action. More...

void	drawCoordinates_ (QPainter &painter, const PeakIndex &peak)
	Draws the coordinates (or coordinate deltas) to the widget's upper left corner. More...

void	drawDeltas_ (QPainter &painter, const PeakIndex &start, const PeakIndex &end)
	Draws the coordinates (or coordinate deltas) to the widget's upper left corner. More...

Protected Member Functions inherited from SpectrumCanvas
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 (QEvent *e) override

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

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 AreaType &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...

PointType	widgetToData_ (double x, double y)
	Convert widget to chart coordinates. More...

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

void	dataToWidget_ (double x, double y, QPoint &point)
	Convert chart to widget coordinates. More...

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

void	recalculateRanges_ (UInt mz_dim, UInt rt_dim, UInt it_dim)
	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	adjustBuffer_ ()
	Changes the size of the paint buffer to the currently required size. More...

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

void	drawText_ (QPainter &painter, 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...

void	popIncompleteLayer_ (const QString &error_message="")

LayerData &	getLayer_ (Size index)
	Returns the layer with index `index`. More...

LayerData &	getCurrentLayer_ ()
	Returns the currently active layer. 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...

Reimplemented QT events
ExperimentType	projection_mz_
	m/z projection data More...

ExperimentType	projection_rt_
	RT projection data. More...

PeakIndex	selected_peak_
	the nearest peak/feature to the mouse cursor More...

PeakIndex	measurement_start_
	start peak/feature of measuring mode More...

MultiGradient	linear_gradient_
	stores the linear color gradient for non-log modes More...

double	pen_size_min_
	minimum number of pixels for one data point More...

double	pen_size_max_
	maximum number of pixels for one data point More...

double	canvas_coverage_min_
	minimum coverage of the canvas required; if lower, points are upscaled in size More...

void	mousePressEvent (QMouseEvent *e) override

void	mouseReleaseEvent (QMouseEvent *e) override

void	mouseMoveEvent (QMouseEvent *e) override

void	paintEvent (QPaintEvent *e) override

void	contextMenuEvent (QContextMenuEvent *e) override

void	keyPressEvent (QKeyEvent *e) override

void	keyReleaseEvent (QKeyEvent *e) override

void	mouseDoubleClickEvent (QMouseEvent *e) override

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

void	paintDots_ (Size layer_index, QPainter &p)
	Paints individual peaks. More...

void	paintAllIntensities_ (Size layer_index, double pen_width, QPainter &painter)

void	paintMaximumIntensities_ (Size layer_index, Size rt_pixel_count, Size mz_pixel_count, QPainter &p)
	Paints maximum intensity of individual peaks. More...

void	paintPrecursorPeaks_ (Size layer_index, QPainter &painter)
	Paints the precursor peaks. More...

void	paintFeatureData_ (Size layer_index, QPainter &p)
	Paints feature data. More...

void	paintTraceConvexHulls_ (Size layer_index, QPainter &p)
	Paints convex hulls (one for each mass trace) of a features layer. More...

void	paintFeatureConvexHulls_ (Size layer_index, QPainter &p)
	Paints the convex hulls (one for each feature) of a features layer. More...

void	paintIdentifications_ (Size layer_index, QPainter &p)
	Paints peptide identifications (for idXML and unassigned peptides in featureXML). More...

void	paintConsensusElements_ (Size layer_index, QPainter &p)
	Paints the consensus elements of a consensus features layer. More...

void	paintConsensusElement_ (Size layer_index, const ConsensusFeature &cf, QPainter &p, bool use_buffer)
	Paints one consensus element of a consensus features layer. More...

bool	isConsensusFeatureVisible_ (const ConsensusFeature &ce, Size layer_index)
	checks if any element of a consensus feature is currently visible. More...

void	paintConvexHulls_ (const std::vector< ConvexHull2D > &hulls, bool hasIdentifications, QPainter &p)
	Paints convex hulls (one for each mass trace) for a single feature. More...

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

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

Int	precalculatedColorIndex_ (float val, const MultiGradient &gradient, double snap_factor)
	Returns the position on color `gradient` associated with given intensity. More...

QColor	heightColor_ (float val, const MultiGradient &gradient, double snap_factor)
	Returns the color associated with `val` for the gradient `gradient`. More...

void	dataToWidget_ (double x, double y, QPoint &point)
	Convert chart to widget coordinates. More...

double	adaptPenScaling_ (double ratio_data2pixel, double &pen_size) const
	For a certain dimension: computes the size a data point would need, such that the image reaches a certain coverage. More...

void	recalculateDotGradient_ (Size layer)
	recalculates the dot gradient of a layer More...

void	highlightPeak_ (QPainter &p, const PeakIndex &peak)
	Highlights a single peak and prints coordinates to screen. More...

PeakIndex	findNearestPeak_ (const QPoint &pos)
	Returns the nearest peak to position `pos`. More...

void	paintIcon_ (const QPoint &pos, const QRgb &color, const String &icon, Size s, QPainter &p) const
	Paints a peak icon for feature and consensus feature peaks. More...

virtual void	translateVisibleArea_ (double mzShiftRel, double rtShiftRel)
	translates the visible area by a given offset specified in fractions of current visible area More...

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

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

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

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

void	finishContextMenu_ (QMenu context_menu, QMenu settings_menu)
	Finishes context menu after customization to peaks, features or consensus features. More...

	Spectrum2DCanvas ()
	Default C'tor hidden. More...

Additional Inherited Members
Public Types inherited from SpectrumCanvas
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 LayerData::ExperimentType	ExperimentType
	Main data type (experiment) More...

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

typedef LayerData::ConstExperimentSharedPtrType	ConstExperimentSharedPtrType

typedef LayerData::ODExperimentSharedPtrType	ODExperimentSharedPtrType

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

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

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

typedef LayerData::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...

typedef FeatureMapType::FeatureType	FeatureType
	Feature type. More...

typedef DPosition< 2 >	PointType
	Type of the Points. More...

typedef DRange< 2 >	AreaType
	Types of Ranges/Areas. More...

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

Protected Attributes inherited from SpectrumCanvas
QImage	buffer_
	Buffer that stores the actual peak information. More...

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

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

std::vector< LayerData >	layers_
	Layer data. More...

bool	mz_to_x_axis_
	Stores the mapping of m/z. More...

AreaType	visible_area_
	Stores the currently visible area. More...

DRange< 3 >	overall_data_range_
	Stores the data range (m/z, RT and intensity) of all layers. More...

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

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

std::vector< AreaType >::iterator	zoom_pos_
	The current position in the zoom stack. More...

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

Size	current_layer_
	Stores the index of the currently active layer. More...

SpectrumWidget *	spectrum_widget_
	Back-pointer to the enclosing spectrum widget. More...

QPoint	last_mouse_pos_
	start position of mouse actions More...

double	percentage_factor_
	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_
	External context menu extension. More...

bool	show_timing_
	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...

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

Canvas for 2D-visualization of peak map, feature map and consensus map data.

This widget displays a 2D representation of a set of peaks, features or consensus elements.

The example image shows Spectrum2DCanvas displaying a peak layer and a feature layer.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
default_path	string	.		Default path for loading/storing data.
background_color	string	@#ffffff		Background color.
interpolation_steps	int	1000	min: 1 max: 1000	Number of interpolation steps for peak gradient pre-calculation.
mapping_of_mz_to	string	y_axis	x_axis, y_axis	Determines which axis is the m/z axis.
dot:gradient	string	Linear\|0,@#eeeeee;1,@#ffea00;6,@#ff0000;14,@#aa00ff;23,@#5500ff;100,@#000000		Multi-color gradient for peaks.
dot:feature_icon	string	circle	diamond, square, circle, triangle	Icon used for features and consensus features.
dot:feature_icon_size	int	4	min: 1 max: 999	Icon size used for features and consensus features.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Improvement:: Add RT interpolation mode for high zoom in 2D View (Hiwi)

Improvement:: Snap also to min intensity (Hiwi)

Constructor & Destructor Documentation

◆ Spectrum2DCanvas() [1/2]

Spectrum2DCanvas	(	const Param &	preferences,
		QWidget *	parent = `nullptr`
	)

Default constructor.

◆ ~Spectrum2DCanvas()

~Spectrum2DCanvas ( )

override

Destructor.

◆ Spectrum2DCanvas() [2/2]

Spectrum2DCanvas ( )

private

Default C'tor hidden.

Member Function Documentation

◆ activateLayer

void activateLayer ( Size layer_index )

overrideslot

◆ adaptPenScaling_()

double adaptPenScaling_	(	double	ratio_data2pixel,
		double &	pen_size
	)		const

protected

For a certain dimension: computes the size a data point would need, such that the image reaches a certain coverage.

Internally, this function makes use of the members 'canvas_coverage_min_' (giving the fraction (e.g. 20%) of area which should be covered by data) and 'pen_size_max_' (maximum allowed number of pixels per data point).

Parameters

ratio_data2pixel	The current ratio of #data points vs. # pixels of image
pen_size	In/Out param: gives the initial pen size, and is increased (up to `MAX_PEN_SIZE`) to reach desired coverage given by 'canvas_coverage_min_'

Returns: The factor by which @pen_size increased (gives a hint of how many data points should be merged to avoid overplotting)

◆ collectFragmentScansInArea()

bool collectFragmentScansInArea	(	double	rt_min,
		double	rt_max,
		double	mz_min,
		double	mz_max,
		QAction *	a,
		QMenu *	msn_scans,
		QMenu *	msn_meta
	)

protected

Collects fragment ion scans in the indicated RT/mz area and adds them to the indicated action.

◆ contextMenuEvent()

void contextMenuEvent ( QContextMenuEvent * e )

overrideprotected

◆ currentLayerParametersChanged_

void currentLayerParametersChanged_ ( )

protectedslot

Reacts on changed layer parameters.

◆ dataToWidget_()

void dataToWidget_	(	double	x,
		double	y,
		QPoint &	point
	)

inlineprotected

Convert chart to widget coordinates.

Translates chart coordinates to widget coordinates.

Parameters

x	the chart coordinate x
y	the chart coordinate y
point	returned widget coordinates

◆ drawCoordinates_()

void drawCoordinates_	(	QPainter &	painter,
		const PeakIndex &	peak
	)

protected

Draws the coordinates (or coordinate deltas) to the widget's upper left corner.

◆ drawDeltas_()

void drawDeltas_	(	QPainter &	painter,
		const PeakIndex &	start,
		const PeakIndex &	end
	)

protected

Draws the coordinates (or coordinate deltas) to the widget's upper left corner.

◆ findNearestPeak_()

PeakIndex findNearestPeak_ ( const QPoint & pos )

protected

Returns the nearest peak to position pos.

◆ finishAdding_()

bool finishAdding_ ( )

overrideprotectedvirtual

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

Implements SpectrumCanvas.

◆ finishContextMenu_()

void finishContextMenu_	(	QMenu *	context_menu,
		QMenu *	settings_menu
	)

protected

Finishes context menu after customization to peaks, features or consensus features.

◆ heightColor_()

QColor heightColor_	(	float	val,
		const MultiGradient &	gradient,
		double	snap_factor
	)

inlineprotected

Returns the color associated with val for the gradient gradient.

Takes intensity modes into account.

References MultiGradient::precalculatedColorByIndex().

◆ highlightPeak_()

void highlightPeak_	(	QPainter &	p,
		const PeakIndex &	peak
	)

protected

Highlights a single peak and prints coordinates to screen.

◆ horizontalScrollBarChange

void horizontalScrollBarChange ( int value )

overrideslot

◆ intensityModeChange_()

void intensityModeChange_ ( )

overrideprotectedvirtual

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

Reimplemented from SpectrumCanvas.

◆ isConsensusFeatureVisible_()

bool isConsensusFeatureVisible_	(	const ConsensusFeature &	ce,
		Size	layer_index
	)

protected

checks if any element of a consensus feature is currently visible.

Parameters

layer_index	Index of the layer.
ce	The ConsensusFeature that needs checking

◆ keyPressEvent()

void keyPressEvent ( QKeyEvent * e )

overrideprotected

◆ keyReleaseEvent()

void keyReleaseEvent ( QKeyEvent * e )

overrideprotected

◆ mergeIntoLayer() [1/3]

void mergeIntoLayer	(	Size	i,
		ConsensusMapSharedPtrType	map
	)

Merges the consensus features in map into the features layer i.

◆ mergeIntoLayer() [2/3]

void mergeIntoLayer	(	Size	i,
		FeatureMapSharedPtrType	map
	)

Merges the features in map into the features layer i.

Referenced by TOPPViewBase::addData().

◆ mergeIntoLayer() [3/3]

void mergeIntoLayer	(	Size	i,
		std::vector< PeptideIdentification > &	peptides
	)

Merges the peptide identifications in peptides into the peptide layer i.

◆ mouseDoubleClickEvent()

void mouseDoubleClickEvent ( QMouseEvent * e )

overrideprotected

◆ mouseMoveEvent()

void mouseMoveEvent ( QMouseEvent * e )

overrideprotected

◆ mousePressEvent()

void mousePressEvent ( QMouseEvent * e )

overrideprotected

◆ mouseReleaseEvent()

void mouseReleaseEvent ( QMouseEvent * e )

overrideprotected

◆ paintAllIntensities_()

void paintAllIntensities_	(	Size	layer_index,
		double	pen_width,
		QPainter &	painter
	)

protected

◆ paintConsensusElement_()

void paintConsensusElement_	(	Size	layer_index,
		const ConsensusFeature &	cf,
		QPainter &	p,
		bool	use_buffer
	)

protected

Paints one consensus element of a consensus features layer.

Parameters

layer_index	Index of the layer.
cf	Reference to the feature to be painted.
p	The QPainter to paint on.
use_buffer	Flag to switch between painting on the buffer and screen.

◆ paintConsensusElements_()

void paintConsensusElements_	(	Size	layer_index,
		QPainter &	p
	)

protected

Paints the consensus elements of a consensus features layer.

Parameters

layer_index	Index of the layer.
p	The QPainter to paint on.

◆ paintConvexHulls_()

void paintConvexHulls_	(	const std::vector< ConvexHull2D > &	hulls,
		bool	hasIdentifications,
		QPainter &	p
	)

protected

Paints convex hulls (one for each mass trace) for a single feature.

Parameters

hulls	Reference to convex hull vector.
p	The QPainter to paint on.

◆ paintDots_()

void paintDots_	(	Size	layer_index,
		QPainter &	p
	)

protected

Paints individual peaks.

Calls different painting methods depending on the layer type and the density of displayed peaks

Parameters

layer_index	The index of the layer.
p	The QPainter to paint on.

◆ paintEvent()

void paintEvent ( QPaintEvent * e )

overrideprotected

◆ paintFeatureConvexHulls_()

void paintFeatureConvexHulls_	(	Size	layer_index,
		QPainter &	p
	)

protected

Paints the convex hulls (one for each feature) of a features layer.

Parameters

layer_index	Index of the layer.
p	The QPainter to paint on.

◆ paintFeatureData_()

void paintFeatureData_	(	Size	layer_index,
		QPainter &	p
	)

protected

Paints feature data.

Parameters

layer_index	The index of the layer.
p	The QPainter to paint on.

◆ paintIcon_()

void paintIcon_	(	const QPoint &	pos,
		const QRgb &	color,
		const String &	icon,
		Size	s,
		QPainter &	p
	)		const

protected

Paints a peak icon for feature and consensus feature peaks.

◆ paintIdentifications_()

void paintIdentifications_	(	Size	layer_index,
		QPainter &	p
	)

protected

Paints peptide identifications (for idXML and unassigned peptides in featureXML).

Parameters

layer_index	Index of the layer.
p	The QPainter to paint on.

◆ paintMaximumIntensities_()

void paintMaximumIntensities_	(	Size	layer_index,
		Size	rt_pixel_count,
		Size	mz_pixel_count,
		QPainter &	p
	)

protected

Paints maximum intensity of individual peaks.

Paints the peaks as small ellipses. The peaks are colored according to the selected dot gradient.

Parameters

layer_index	The index of the layer.
rt_pixel_count
mz_pixel_count
p	The QPainter to paint on.

◆ paintPrecursorPeaks_()

void paintPrecursorPeaks_	(	Size	layer_index,
		QPainter &	painter
	)

protected

Paints the precursor peaks.

Parameters

layer_index	The index of the layer.
painter	The QPainter to paint on.

◆ paintTraceConvexHulls_()

void paintTraceConvexHulls_	(	Size	layer_index,
		QPainter &	p
	)

protected

Paints convex hulls (one for each mass trace) of a features layer.

Parameters

layer_index	Index of the layer.
p	The QPainter to paint on.

◆ precalculatedColorIndex_()

Int precalculatedColorIndex_	(	float	val,
		const MultiGradient &	gradient,
		double	snap_factor
	)

inlineprotected

Returns the position on color gradient associated with given intensity.

Takes intensity modes into account.

References OpenMS::IM_NONE, and MultiGradient::precalculatedColorIndex().

◆ recalculateCurrentLayerDotGradient()

void recalculateCurrentLayerDotGradient ( )

recalculates the dot gradient of the active layer

◆ recalculateDotGradient_()

void recalculateDotGradient_ ( Size layer )

protected

recalculates the dot gradient of a layer

◆ recalculateSnapFactor_()

void recalculateSnapFactor_ ( )

overrideprotectedvirtual

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

See also: snap_factors_

Reimplemented from SpectrumCanvas.

◆ removeLayer

void removeLayer ( Size layer_index )

overrideslot

◆ saveCurrentLayer()

void saveCurrentLayer ( bool visible )

overridevirtual

Saves the current layer data.

Parameters

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

Implements SpectrumCanvas.

◆ showCurrentLayerPreferences()

void showCurrentLayerPreferences ( )

overridevirtual

Shows the preferences dialog of the active layer.

Implements SpectrumCanvas.

◆ showCurrentPeaksAs3D

void showCurrentPeaksAs3D ( )

signal

Requests to display all spectra in 3D plot.

◆ showProjectionHorizontal

void showProjectionHorizontal ( ExperimentSharedPtrType )

signal

Sets the data for the horizontal projection.

◆ showProjectionInfo

void showProjectionInfo	(	int	,
		double	,
		double
	)

signal

Shows the number of peaks and the intensity sum of the projection.

◆ showProjectionVertical

void showProjectionVertical ( ExperimentSharedPtrType )

signal

Sets the data for the vertical projection.

◆ showSpectrumAs1D [1/2]

void showSpectrumAs1D ( int index )

signal

Requests to display the spectrum with index index in 1D.

◆ showSpectrumAs1D [2/2]

void showSpectrumAs1D ( std::vector< int, std::allocator< int > > indices )

signal

◆ toggleProjections

void toggleProjections ( )

signal

Signal emitted when the projections are to be shown/hidden.

◆ translateBackward_()

void translateBackward_ ( )

overrideprotectedvirtual

Translation bound to the 'Down' key.

Reimplemented from SpectrumCanvas.

◆ translateForward_()

void translateForward_ ( )

overrideprotectedvirtual

Translation bound to the 'Up' key.

Reimplemented from SpectrumCanvas.

◆ translateLeft_()

void translateLeft_ ( Qt::KeyboardModifiers m )

overrideprotectedvirtual

Translation bound to the 'Left' key.

Reimplemented from SpectrumCanvas.

◆ translateRight_()

void translateRight_ ( Qt::KeyboardModifiers m )

overrideprotectedvirtual

Translation bound to the 'Right' key.

Reimplemented from SpectrumCanvas.

◆ translateVisibleArea_()

virtual void translateVisibleArea_	(	double	mzShiftRel,
		double	rtShiftRel
	)

protectedvirtual

translates the visible area by a given offset specified in fractions of current visible area

◆ updateLayer

void updateLayer ( Size i )

overrideslot

◆ updateProjections

void updateProjections ( )

slot

Updates the projection data and emits some related signals.

Emitted signals are showProjectionHorizontal(ExperimentSharedPtrType, Spectrum1DCanvas::DrawModes, SpectrumCanvas::IntensityModes) and showProjectionVertical(ExperimentSharedPtrType, Spectrum1DCanvas::DrawModes, SpectrumCanvas::IntensityModes).

See also: projection_mz_; projection_rt_

◆ updateScrollbars_()

void updateScrollbars_ ( )

overrideprotectedvirtual

Updates the scroll bars.

Updates the scrollbars after a change of the visible area.

Reimplemented from SpectrumCanvas.

◆ verticalScrollBarChange

void verticalScrollBarChange ( int value )

overrideslot

Member Data Documentation

◆ canvas_coverage_min_

double canvas_coverage_min_

protected

minimum coverage of the canvas required; if lower, points are upscaled in size

◆ linear_gradient_

MultiGradient linear_gradient_

protected

stores the linear color gradient for non-log modes

◆ measurement_start_

PeakIndex measurement_start_

protected

start peak/feature of measuring mode

◆ pen_size_max_

double pen_size_max_

protected

maximum number of pixels for one data point

◆ pen_size_min_

double pen_size_min_

protected

minimum number of pixels for one data point

◆ projection_mz_

ExperimentType projection_mz_

protected

m/z projection data

◆ projection_rt_

ExperimentType projection_rt_

protected

RT projection data.

◆ selected_peak_

PeakIndex selected_peak_

protected

the nearest peak/feature to the mouse cursor

Public Slots

Signals

Public Member Functions

Protected Slots

Protected Member Functions

Reimplemented QT events

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Spectrum2DCanvas() [1/2]

◆ ~Spectrum2DCanvas()

◆ Spectrum2DCanvas() [2/2]

Member Function Documentation

◆ activateLayer

◆ adaptPenScaling_()

◆ collectFragmentScansInArea()

◆ contextMenuEvent()

◆ currentLayerParametersChanged_

◆ dataToWidget_()

◆ drawCoordinates_()

◆ drawDeltas_()

◆ findNearestPeak_()

◆ finishAdding_()

◆ finishContextMenu_()

◆ heightColor_()

◆ highlightPeak_()

◆ horizontalScrollBarChange

◆ intensityModeChange_()

◆ isConsensusFeatureVisible_()

◆ keyPressEvent()

◆ keyReleaseEvent()

◆ mergeIntoLayer() [1/3]

◆ mergeIntoLayer() [2/3]

◆ mergeIntoLayer() [3/3]

◆ mouseDoubleClickEvent()

◆ mouseMoveEvent()

◆ mousePressEvent()

◆ mouseReleaseEvent()

◆ paintAllIntensities_()

◆ paintConsensusElement_()

◆ paintConsensusElements_()

◆ paintConvexHulls_()

◆ paintDots_()

◆ paintEvent()

◆ paintFeatureConvexHulls_()

◆ paintFeatureData_()

◆ paintIcon_()

◆ paintIdentifications_()

◆ paintMaximumIntensities_()

◆ paintPrecursorPeaks_()

◆ paintTraceConvexHulls_()

◆ precalculatedColorIndex_()

◆ recalculateCurrentLayerDotGradient()

◆ recalculateDotGradient_()

◆ recalculateSnapFactor_()

◆ removeLayer

◆ saveCurrentLayer()

◆ showCurrentLayerPreferences()

◆ showCurrentPeaksAs3D

◆ showProjectionHorizontal

◆ showProjectionInfo

◆ showProjectionVertical

◆ showSpectrumAs1D [1/2]

◆ showSpectrumAs1D [2/2]

◆ toggleProjections

◆ translateBackward_()

◆ translateForward_()

◆ translateLeft_()

◆ translateRight_()

◆ translateVisibleArea_()

◆ updateLayer

◆ updateProjections

◆ updateScrollbars_()

◆ verticalScrollBarChange

Member Data Documentation

◆ canvas_coverage_min_

◆ linear_gradient_

◆ measurement_start_

◆ pen_size_max_

◆ pen_size_min_