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

#include <OpenMS/VISUAL/Spectrum2DCanvas.h>

Inheritance diagram for Spectrum2DCanvas:

Public Slots
void	activateLayer (Size layer_index)
	change the active layer (the one that is used for selecting and so on)
void	removeLayer (Size layer_index)
	removes the layer with index `layer_index`
virtual void	updateLayer (Size i)
	Updates layer `i` when the data in the corresponding file changes.
virtual void	horizontalScrollBarChange (int value)
	Notifies the canvas that the horizontal scollbar has been moved.
virtual void	verticalScrollBarChange (int value)
	Notifies the canvas that the vertical scollbar has been moved.
void	updateProjections ()
	Updates the projection data and emits some related signals.
Signals
void	showProjectionHorizontal (ExperimentSharedPtrType, Spectrum1DCanvas::DrawModes)
	Sets the data for the horizontal projection.
void	showProjectionVertical (ExperimentSharedPtrType, Spectrum1DCanvas::DrawModes)
	Sets the data for the vertical projection.
void	showProjectionInfo (int, double, double)
	Shows the number of peaks and the intensity sum of the projection.
void	toggleProjections ()
	Signal emitted when the projections are to be shown/hidden.
void	showSpectrumAs1D (int index)
	Requests to display the spectrum with index `index` in 1D.
void	showSpectrumAs1D (std::vector< int, std::allocator< int > > indices)
void	showCurrentPeaksAs3D ()
	Requests to display all spectra in 3D plot.
Public Member Functions
	Spectrum2DCanvas (const Param &preferences, QWidget *parent=0)
	Default constructor.
	~Spectrum2DCanvas ()
	Destructor.
virtual void	showCurrentLayerPreferences ()
	Shows the preferences dialog of the active layer.
virtual void	saveCurrentLayer (bool visible)
	Saves the current layer data.
void	mergeIntoLayer (Size i, FeatureMapSharedPtrType map)
	Merges the features in `map` into the features layer `i`.
void	mergeIntoLayer (Size i, ConsensusMapSharedPtrType map)
	Merges the consensus features in `map` into the features layer `i`.
void	mergeIntoLayer (Size i, std::vector< PeptideIdentification > &peptides)
	Merges the peptide identifications in `peptides` into the peptide layer `i`.
void	recalculateCurrentLayerDotGradient ()
	recalculates the dot gradient of the active layer
Protected Slots
void	currentLayerParametersChanged_ ()
	Reacts on changed layer paramters.
Protected Member Functions
bool	finishAdding_ ()
	Method that is called when a new layer has been added.
void	drawCoordinates_ (QPainter &painter, const PeakIndex &peak)
	Draws the coordinates (or coordinate deltas) to the widget's upper left corner.
void	drawDeltas_ (QPainter &painter, const PeakIndex &start, const PeakIndex &end)
	Draws the coordinates (or coordinate deltas) to the widget's upper left corner.
virtual void	updateScrollbars_ ()
	Updates the scroll bars.
void	paintDots_ (Size layer_index, QPainter &p)
	Paints individual peaks.
void	paintAllIntensities_ (Size layer_index, DoubleReal 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.
void	paintPrecursorPeaks_ (Size layer_index, QPainter &painter)
	Paints the precursor peaks.
void	paintFeatureData_ (Size layer_index, QPainter &p)
	Paints feature data.
void	paintTraceConvexHulls_ (Size layer_index, QPainter &p)
	Paints convex hulls (one for each mass trace) of a features layer.
void	paintFeatureConvexHulls_ (Size layer_index, QPainter &p)
	Paints the convex hulls (one for each feature) of a features layer.
void	paintIdentifications_ (Size layer_index, QPainter &p)
	Paints peptide identifications (for idXML and unassigned peptides in featureXML).
void	paintConsensusElements_ (Size layer_index, QPainter &p)
	Paints the consensus elements of a consensus features layer.
void	paintConsensusElement_ (Size layer_index, const ConsensusFeature &cf, QPainter &p, bool use_buffer)
	Paints one consensus element of a consensus features layer.
bool	isConsensusFeatureVisible_ (const ConsensusFeature &ce, Size layer_index)
	checks if any element of a consensus feature is currently visible.
void	paintConvexHulls_ (const std::vector< ConvexHull2D > &hulls, bool hasIdentifications, QPainter &p)
	Paints convex hulls (one for each mass trace) for a single feature.
virtual void	intensityModeChange_ ()
	This method is called whenever the intensity mode changes. Reimplement if you need to react on such changes.
virtual void	recalculateSnapFactor_ ()
	REcalculates the intensity scaling factor for 'snap to maximum intensity mode'.
Int	precalculatedColorIndex_ (Real val, const MultiGradient &gradient, DoubleReal snap_factor)
	Returns the position on color `gradient` associated with given intensity .
QColor	heightColor_ (Real val, const MultiGradient &gradient, DoubleReal snap_factor)
	Returns the color associated with `val` for the gradient `gradient`.
void	dataToWidget_ (DoubleReal x, DoubleReal y, QPoint &point)
	Convert chart to widget coordinates.
void	recalculateDotGradient_ (Size layer)
	recalculates the dot gradient of a layer
void	highlightPeak_ (QPainter &p, const PeakIndex &peak)
	Highlights a single peak and prints coordinates to screen.
PeakIndex	findNearestPeak_ (const QPoint &pos)
	Returns the nearest peak to position `pos`.
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.
virtual void	translateVisibleArea_ (DoubleReal mzShiftRel, DoubleReal rtShiftRel)
	translates the visible area by a given offset specified in fractions of current visible area
virtual void	translateLeft_ ()
	Translation bound to the 'Left' key.
virtual void	translateRight_ ()
	Translation bound to the 'Rightt' key.
virtual void	translateForward_ ()
	Translation bound to the 'Up' key.
virtual void	translateBackward_ ()
	Translation bound to the 'Down' key.
void	finishContextMenu_ (QMenu context_menu, QMenu settings_menu)
	Finishes context menu after customization to peaks, features or consensus features.
Reimplemented QT events

void	mousePressEvent (QMouseEvent *e)
void	mouseReleaseEvent (QMouseEvent *e)
void	mouseMoveEvent (QMouseEvent *e)
void	paintEvent (QPaintEvent *e)
void	contextMenuEvent (QContextMenuEvent *e)
void	keyPressEvent (QKeyEvent *e)
void	keyReleaseEvent (QKeyEvent *e)
void	mouseDoubleClickEvent (QMouseEvent *e)
Protected Attributes
ExperimentType	projection_mz_
	m/z projection data
ExperimentType	projection_rt_
	RT projection data.
PeakIndex	selected_peak_
	the nearest peak/feature to the mouse cursor
PeakIndex	measurement_start_
	start peak/feature of measuring mode

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 interploation steps for peak gradient precalculation.
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	(	const Param &	preferences,
		QWidget *	parent = `0`
	)

Default constructor.

~Spectrum2DCanvas ( )

Destructor.

Member Function Documentation

void activateLayer ( Size layer_index ) [virtual, slot]

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

Implements SpectrumCanvas.

void contextMenuEvent ( QContextMenuEvent * e ) [protected]

void currentLayerParametersChanged_ ( ) [protected, slot]

Reacts on changed layer paramters.

void dataToWidget_	(	DoubleReal	x,
		DoubleReal	y,
		QPoint &	point
	)			`[inline, protected]`

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

Reimplemented from SpectrumCanvas.

void drawCoordinates_	(	QPainter &	painter,
		const PeakIndex &	peak
	)			`[protected]`

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

void drawDeltas_	(	QPainter &	painter,
		const PeakIndex &	start,
		const PeakIndex &	end
	)			`[protected]`

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

PeakIndex findNearestPeak_ ( const QPoint & pos ) [protected]

Returns the nearest peak to position pos.

bool finishAdding_ ( ) [protected, virtual]

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

Implements SpectrumCanvas.

void finishContextMenu_	(	QMenu *	context_menu,
		QMenu *	settings_menu
	)			`[protected]`

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

QColor heightColor_	(	Real	val,
		const MultiGradient &	gradient,
		DoubleReal	snap_factor
	)			`[inline, protected]`

Returns the color associated with val for the gradient gradient.

Takes intensity modes into account.

References MultiGradient::precalculatedColorByIndex().

void highlightPeak_	(	QPainter &	p,
		const PeakIndex &	peak
	)			`[protected]`

Highlights a single peak and prints coordinates to screen.

virtual void horizontalScrollBarChange ( int value ) [virtual, slot]

Notifies the canvas that the horizontal scollbar has been moved.

Reimplement this slot to react on scrollbar events.

Reimplemented from SpectrumCanvas.

virtual void intensityModeChange_ ( ) [protected, virtual]

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

Reimplemented from SpectrumCanvas.

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

void keyPressEvent ( QKeyEvent * e ) [protected]

Reimplemented from SpectrumCanvas.

void keyReleaseEvent ( QKeyEvent * e ) [protected]

Reimplemented from SpectrumCanvas.

void mergeIntoLayer	(	Size	i,
		ConsensusMapSharedPtrType	map
	)

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

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

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

void mergeIntoLayer	(	Size	i,
		FeatureMapSharedPtrType	map
	)

Merges the features in map into the features layer i.

Referenced by TOPPViewBase::addData().

void mouseDoubleClickEvent ( QMouseEvent * e ) [protected]

void mouseMoveEvent ( QMouseEvent * e ) [protected]

void mousePressEvent ( QMouseEvent * e ) [protected]

void mouseReleaseEvent ( QMouseEvent * e ) [protected]

void paintAllIntensities_	(	Size	layer_index,
		DoubleReal	pen_width,
		QPainter &	painter
	)			`[protected]`

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.

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.

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.

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.

void paintEvent ( QPaintEvent * e ) [protected]

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.

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.

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.

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.

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.
	p	The QPainter to paint on.

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.

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.

Int precalculatedColorIndex_	(	Real	val,
		const MultiGradient &	gradient,
		DoubleReal	snap_factor
	)			`[inline, protected]`

Returns the position on color gradient associated with given intensity .

Takes intensity modes into account.

References MultiGradient::precalculatedColorIndex().

void recalculateCurrentLayerDotGradient ( )

recalculates the dot gradient of the active layer

Referenced by TOPPViewBase::setIntensityMode().

void recalculateDotGradient_ ( Size layer ) [protected]

recalculates the dot gradient of a layer

virtual void recalculateSnapFactor_ ( ) [protected, virtual]

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

See also:: snap_factors_

Reimplemented from SpectrumCanvas.

void removeLayer ( Size layer_index ) [virtual, slot]

removes the layer with index layer_index

Implements SpectrumCanvas.

virtual void saveCurrentLayer ( bool visible ) [virtual]

Saves the current layer data.

Parameters:

visible

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

Implements SpectrumCanvas.

virtual void showCurrentLayerPreferences ( ) [virtual]

Shows the preferences dialog of the active layer.

Implements SpectrumCanvas.

void showCurrentPeaksAs3D ( ) [signal]

Requests to display all spectra in 3D plot.

void showProjectionHorizontal	(	ExperimentSharedPtrType	,
		Spectrum1DCanvas::DrawModes
	)			`[signal]`

Sets the data for the horizontal projection.

void showProjectionInfo	(	int	,
		double	,
		double
	)			`[signal]`

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

void showProjectionVertical	(	ExperimentSharedPtrType	,
		Spectrum1DCanvas::DrawModes
	)			`[signal]`

Sets the data for the vertical projection.

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

void showSpectrumAs1D ( int index ) [signal]

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

void toggleProjections ( ) [signal]

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

virtual void translateBackward_ ( ) [protected, virtual]

Translation bound to the 'Down' key.

Reimplemented from SpectrumCanvas.

virtual void translateForward_ ( ) [protected, virtual]

Translation bound to the 'Up' key.

Reimplemented from SpectrumCanvas.

virtual void translateLeft_ ( ) [protected, virtual]

Translation bound to the 'Left' key.

Reimplemented from SpectrumCanvas.

virtual void translateRight_ ( ) [protected, virtual]

Translation bound to the 'Rightt' key.

Reimplemented from SpectrumCanvas.

virtual void translateVisibleArea_	(	DoubleReal	mzShiftRel,
		DoubleReal	rtShiftRel
	)			`[protected, virtual]`

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

virtual void updateLayer ( Size i ) [virtual, slot]

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

Implements SpectrumCanvas.

void updateProjections ( ) [slot]

Updates the projection data and emits some related signals.

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

See also:: projection_mz_; projection_rt_

virtual void updateScrollbars_ ( ) [protected, virtual]

Updates the scroll bars.

Updates the scrollbars after a change of the visible area.

Reimplemented from SpectrumCanvas.

virtual void verticalScrollBarChange ( int value ) [virtual, slot]

Notifies the canvas that the vertical scollbar has been moved.

Reimplement this slot to react on scrollbar events.

Reimplemented from SpectrumCanvas.

Member Data Documentation

PeakIndex measurement_start_ [protected]

start peak/feature of measuring mode

Reimplemented from SpectrumCanvas.

ExperimentType projection_mz_ [protected]

m/z projection data

ExperimentType projection_rt_ [protected]

RT projection data.

PeakIndex selected_peak_ [protected]

the nearest peak/feature to the mouse cursor

Reimplemented from SpectrumCanvas.

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:58 using doxygen 1.7.1

Spectrum2DCanvas Class Reference [Spectrum visualizaion widgets]

Public Slots

Signals

Public Member Functions

Protected Slots

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

Spectrum2DCanvas Class Reference
[Spectrum visualizaion widgets]