Canvas for 3D-visualization of peak map data. More...

#include <OpenMS/VISUAL/Spectrum3DCanvas.h>

Inheritance diagram for Spectrum3DCanvas:

Collaboration diagram for Spectrum3DCanvas:

Public Types
enum	ShadeModes { SHADE_FLAT = 0, SHADE_SMOOTH = 1 }
	Different shade modes. More...

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...

Public Member Functions
	Spectrum3DCanvas (const Param &preferences, QWidget *parent=nullptr)
	Constructor. More...

	~Spectrum3DCanvas () override
	Destructor. More...

Spectrum3DOpenGLCanvas *	openglwidget ()
	returns the Spectrum3DOpenGLcanvas 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...

Friends
class	Spectrum3DOpenGLCanvas

Reimplemented Qt events
Spectrum3DOpenGLCanvas *	openglcanvas_
	pointer to the SpectrumOpenGLCanvas implementation More...

bool	legend_shown_
	whether the legend is shown or not More...

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

void	resizeEvent (QResizeEvent *e) override

void	contextMenuEvent (QContextMenuEvent *e) override

bool	isLegendShown () const
	Returns if the legend is shown. More...

void	showLegend (bool)
	Shows/hides the legend. 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	showCurrentPeaksAs2D ()
	Requests to display all spectra in 2D plot. More...

void	activateLayer (Size layer_index) override

void	removeLayer (Size layer_index) override

void	updateLayer (Size i) override

void	intensityModeChange_ () override

void	currentLayerParamtersChanged_ ()
	Reacts on changed layer parameters. More...

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

void	update_ (const char *caller_name=nullptr) override
	Updates the displayed data. 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...

Additional Inherited Members
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 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...

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 Slots inherited from SpectrumCanvas
void	updateCursor_ ()
	Updates the cursor according to the current action mode. 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	intensityModeChange_ ()
	This method is called whenever the intensity mode changes. Reimplement if you need to react on such changes. More...

virtual void	changeVisibleArea_ (const AreaType &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...

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...

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

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...

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 3D-visualization of peak map data.

The Spectrum3DCanvas uses the helper class Spectrum3DOpenGLCanvas for the actual 3D rendering. Deriving Spectrum3DCanvas directly from QGLWidget is not possible due to the "Deadly Diamond" shape of inheritance.

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
dot:shade_mode	int	1	min: 0 max: 1	Shade mode: single-color ('flat') or gradient peaks ('smooth').
dot:gradient	string	Linear\|0,@#ffea00;6,@#ff0000;14,@#aa00ff;23,@#5500ff;100,@#000000		Peak color gradient.
dot:interpolation_steps	int	1000	min: 1 max: 1000	Interpolation steps for peak color gradient precalculation.
dot:line_width	int	2	min: 1 max: 99	Line width for peaks.

Note:

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

Member Enumeration Documentation

◆ ShadeModes

enum ShadeModes

Different shade modes.

Enumerator
SHADE_FLAT
SHADE_SMOOTH

Constructor & Destructor Documentation

◆ Spectrum3DCanvas()

Spectrum3DCanvas	(	const Param &	preferences,
		QWidget *	parent = `nullptr`
	)

Constructor.

◆ ~Spectrum3DCanvas()

~Spectrum3DCanvas ( )

override

Destructor.

Member Function Documentation

◆ activateLayer

void activateLayer ( Size layer_index )

overrideslot

◆ contextMenuEvent()

void contextMenuEvent ( QContextMenuEvent * e )

override

◆ currentLayerParamtersChanged_

void currentLayerParamtersChanged_ ( )

protectedslot

Reacts on changed layer parameters.

◆ finishAdding_()

bool finishAdding_ ( )

overrideprotectedvirtual

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

Implements SpectrumCanvas.

◆ intensityModeChange_

void intensityModeChange_ ( )

overrideslot

◆ isLegendShown()

bool isLegendShown ( ) const

Returns if the legend is shown.

◆ openglwidget()

Spectrum3DOpenGLCanvas* openglwidget ( )

returns the Spectrum3DOpenGLcanvas

Referenced by TOPPViewBase::showCurrentPeaksAs3D().

◆ removeLayer

void removeLayer ( Size layer_index )

overrideslot

◆ resizeEvent()

void resizeEvent ( QResizeEvent * e )

override

◆ 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.

◆ showCurrentPeaksAs2D

void showCurrentPeaksAs2D ( )

signal

Requests to display all spectra in 2D plot.

◆ showLegend()

void showLegend ( bool )

Shows/hides the legend.

◆ 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.

◆ update_()

void update_ ( const char * caller_name = nullptr )

overrideprotectedvirtual

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 from SpectrumCanvas.

◆ updateLayer

void updateLayer ( Size i )

overrideslot

Friends And Related Function Documentation

◆ Spectrum3DOpenGLCanvas

friend class Spectrum3DOpenGLCanvas

friend

Member Data Documentation

◆ legend_shown_

bool legend_shown_

protected

whether the legend is shown or not

◆ linear_gradient_

MultiGradient linear_gradient_

protected

stores the linear color gradient for non-log modes

◆ openglcanvas_

Spectrum3DOpenGLCanvas* openglcanvas_

pointer to the SpectrumOpenGLCanvas implementation

Public Types

Public Member Functions

Friends

Reimplemented Qt events

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ ShadeModes

Constructor & Destructor Documentation

◆ Spectrum3DCanvas()

◆ ~Spectrum3DCanvas()

Member Function Documentation

◆ activateLayer

◆ contextMenuEvent()

◆ currentLayerParamtersChanged_

◆ finishAdding_()

◆ intensityModeChange_

◆ isLegendShown()

◆ openglwidget()

◆ removeLayer

◆ resizeEvent()

◆ saveCurrentLayer()

◆ showCurrentLayerPreferences()

◆ showCurrentPeaksAs2D

◆ showLegend()

◆ translateBackward_()

◆ translateForward_()

◆ translateLeft_()

◆ translateRight_()

◆ update_()

◆ updateLayer

Friends And Related Function Documentation

◆ Spectrum3DOpenGLCanvas

Member Data Documentation

◆ legend_shown_

◆ linear_gradient_

◆ openglcanvas_