Canvas for visualization of one or several spectra. More...

#include <OpenMS/VISUAL/Spectrum1DCanvas.h>

Inheritance diagram for Spectrum1DCanvas:

Public Types
enum	LabelMode { LM_XABSOLUTE_YABSOLUTE, LM_XPERCENT_YABSOLUTE, LM_XABSOLUTE_YPERCENT, LM_XPERCENT_YPERCENT }
	Label modes (percentage or absolut) of x axis and y axis. More...
enum	DrawModes { DM_PEAKS, DM_CONNECTEDLINES }
	Enumerate all avaiable paint styles. More...
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.
void	setVisibleArea (DRange< 2 > range)
	Sets the visible area.
virtual void	horizontalScrollBarChange (int value)
	Notifies the canvas that the horizontal scollbar has been moved.
Signals
void	showCurrentPeaksAs2D ()
	Requests to display all spectra in 2D plot.
void	showCurrentPeaksAs3D ()
	Requests to display all spectra in 3D plot.
Public Member Functions
	Spectrum1DCanvas (const Param &preferences, QWidget *parent=0)
	Default constructor.
virtual	~Spectrum1DCanvas ()
	Destructor.
DrawModes	getDrawMode () const
	Returns the draw mode of the current layer.
void	setDrawMode (DrawModes mode)
	Sets draw mode of the current layer.
virtual void	showCurrentLayerPreferences ()
	Shows the preferences dialog of the active layer.
virtual void	saveCurrentLayer (bool visible)
	Saves the current layer data.
bool	flippedLayersExist ()
	Returns whether flipped layers exist or not.
void	flipLayer (Size index)
	Flips the layer with `index` up/downwards.
bool	mirrorModeActive ()
	Returns whether this widget is currently in mirror mode.
void	setMirrorModeActive (bool b)
	Sets whether this widget is currently in mirror mode.
void	dataToWidget (const PeakType &peak, QPoint &point, bool flipped=false, bool percentage=true)
	For convenience - calls dataToWidget.
void	dataToWidget (DoubleReal x, DoubleReal y, QPoint &point, bool flipped=false, bool percentage=false)
	Calls SpectrumCanvas::dataToWidget_(), takes mirror mode into account.
PointType	widgetToData (const QPoint &pos, bool percentage=false)
	For convenience - calls widgetToData.
PointType	widgetToData (DoubleReal x, DoubleReal y, bool percentage=false)
	Calls SpectrumCanvas::widgetToData_(), takes mirror mode into account.
Annotation1DItem *	addPeakAnnotation (PeakIndex peak_index, QString text, QColor color)
	----- Annotations
void	drawAnnotations (Size layer_index, QPainter &painter)
	Draws all annotation items of `layer_index` on `painter`.
void	performAlignment (Size layer_index_1, Size layer_index_2, const Param &param)
	----- Alignment
void	resetAlignment ()
	Resets alignment_.
void	drawAlignment (QPainter &painter)
	Draws the alignment on `painter`.
Size	getAlignmentSize ()
	Returns the number of aligned pairs of peaks.
DoubleReal	getAlignmentScore ()
	Returns the score of the alignment.
std::vector< std::pair< Size, Size > >	getAlignedPeaksIndices ()
	Returns aligned_peaks_indices_.
void	activateSpectrum (Size index, bool repaint=true)
	Sets current spectrum index of current layer to `index`.
void	setSwappedAxis (bool swapped)
	is the widget shown vertically? (for projections)
void	setCurrentLayerPeakPenStyle (Qt::PenStyle ps)
	Set's the Qt PenStyle of the active layer.
void	paint (QPainter paint_device, QPaintEvent e)
	Actual painting takes place here.
Protected Slots
void	currentLayerParamtersChanged_ ()
	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.
void	changeVisibleArea_ (double lo, double hi, bool repaint=true, bool add_to_stack=false)
	Changes visible area interval.
void	drawHighlightedPeak_ (Size layer_index, const PeakIndex &peak, QPainter &painter, bool draw_elongation=false)
	Draws a highlighted peak; if draw_elongation is true, the elongation line is drawn (for measuring).
void	drawDashedLine_ (const QPoint &from, const QPoint &to, QPainter &painter)
	Draws a dashed line using the highlighted peak color parameter.
void	updatePercentageFactor_ (Size layer_index)
	Recalculates the current scale factor based on the specified layer (= 1.0 if intensity mode != IM_PERCENTAGE).
virtual void	changeVisibleArea_ (const AreaType &new_area, bool repaint=true, bool add_to_stack=false)
	Sets the visible area.
virtual void	recalculateSnapFactor_ ()
	REcalculates the intensity scaling factor for 'snap to maximum intensity mode'.
virtual void	updateScrollbars_ ()
	Updates the scroll bars.
virtual void	intensityModeChange_ ()
	This method is called whenever the intensity mode changes. Reimplement if you need to react on such changes.
PeakIndex	findPeakAtPosition_ (QPoint)
	Find peak next to the given position.
void	addUserLabelAnnotation_ (const QPoint &screen_position)
	Shows dialog and calls addLabelAnnotation_.
void	addLabelAnnotation_ (const QPoint &screen_position, QString label_text)
	Adds an annotation item at the given screen position.
void	addUserPeakAnnotation_ (PeakIndex near_peak)
	Shows dialog and calls addPeakAnnotation_.
void	ensureAnnotationsWithinDataRange_ ()
	Ensure that all annotations are within data range.
virtual void	zoomForward_ ()
	Go forward in zoom history.
virtual void	translateLeft_ ()
	Translation bound to the 'Left' key.
virtual void	translateRight_ ()
	Translation bound to the 'Rightt' key.
virtual void	paintGridLines_ (QPainter &painter)
	Helper function to paint grid lines.
Reimplemented QT events

void	paintEvent (QPaintEvent *e)
void	mousePressEvent (QMouseEvent *e)
void	mouseReleaseEvent (QMouseEvent *e)
void	mouseMoveEvent (QMouseEvent *e)
void	keyPressEvent (QKeyEvent *e)
void	contextMenuEvent (QContextMenuEvent *e)
Protected Attributes
std::vector< DrawModes >	draw_modes_
	Draw modes (for each spectrum).
std::vector< Qt::PenStyle >	peak_penstyle_
	Draw style.
QPoint	measurement_start_point_
	start point of "ruler" for measure mode
bool	mirror_mode_
	Indicates whether this widget is currently in mirror mode.
bool	moving_annotations_
	Indicates whether annotation items are just being moved on the canvas.
bool	show_alignment_
	Indicates whether an alignment is currently visualized.
Size	alignment_layer_1_
	Layer index of the first alignment layer.
Size	alignment_layer_2_
	Layer index of the second alignment layer.
std::vector< std::pair < DoubleReal, DoubleReal > >	aligned_peaks_mz_delta_
	Stores the alignment as MZ values of pairs of aligned peaks in both spectra.
std::vector< std::pair< Size, Size > >	aligned_peaks_indices_
	Stores the peak indizes of pairs of aligned peaks in both spectra.
DoubleReal	alignment_score_
	Stores the score of the last alignment.
bool	is_swapped_
	is this widget showing data with swapped m/z and RT axis? (for drawCoordinates_ only)

Detailed Description

Canvas for visualization of one or several spectra.

The example image shows Spectrum1DCanvas displaying a raw data layer and a peak data layer.

Todo:: Use spectrum StringDataArray with name 'label' for peak annotations (Hiwi, Johannes)

Parameters of this class are:

Name	Type	Default	Description
default_path	string	.	Default path for loading/storing data.
highlighted_peak_color	string	@#ff0000	Highlighted peak color.
icon_color	string	@#000000	Peak icon color.
peak_color	string	@#0000ff	Peak color.
annotation_color	string	@#000055	Annotation color.
background_color	string	@#ffffff	Background color.
show_legend	string	false	Annotate each layer with its name on the canvas.

Note:

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

Member Enumeration Documentation

enum DrawModes

Enumerate all avaiable paint styles.

Enumerator:

DM_PEAKS
DM_CONNECTEDLINES

enum LabelMode

Label modes (percentage or absolut) of x axis and y axis.

Enumerator:

LM_XABSOLUTE_YABSOLUTE
LM_XPERCENT_YABSOLUTE
LM_XABSOLUTE_YPERCENT
LM_XPERCENT_YPERCENT

Constructor & Destructor Documentation

Spectrum1DCanvas	(	const Param &	preferences,
		QWidget *	parent = `0`
	)

Default constructor.

virtual ~Spectrum1DCanvas ( ) [virtual]

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 activateSpectrum	(	Size	index,
		bool	repaint = `true`
	)

Sets current spectrum index of current layer to index.

Referenced by TOPPViewBase::addData().

void addLabelAnnotation_	(	const QPoint &	screen_position,
		QString	label_text
	)			`[protected]`

Adds an annotation item at the given screen position.

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

----- Annotations

Add an annotation item for the given peak

void addUserLabelAnnotation_ ( const QPoint & screen_position ) [protected]

Shows dialog and calls addLabelAnnotation_.

void addUserPeakAnnotation_ ( PeakIndex near_peak ) [protected]

Shows dialog and calls addPeakAnnotation_.

void changeVisibleArea_	(	double	lo,
		double	hi,
		bool	repaint = `true`,
		bool	add_to_stack = `false`
	)			`[protected]`

Changes visible area interval.

This method is for convenience only. It calls changeVisibleArea_(const AreaType&, bool, bool) .

virtual void changeVisibleArea_	(	const AreaType &	new_area,
		bool	repaint = `true`,
		bool	add_to_stack = `false`
	)			`[protected, virtual]`

Sets the visible area.

Changes the visible area, adjustes the zoom stack and notifies interested clients about the change. If parts of the area are outside of the data area, the new area will be adjusted.

Parameters:

	new_area	The new visible area.
	repaint	if repainting of the widget should ne triggered
	add_to_stack	If the new area is to add to the zoom_stack_

Reimplemented from SpectrumCanvas.

void contextMenuEvent ( QContextMenuEvent * e ) [protected]

void currentLayerParamtersChanged_ ( ) [protected, slot]

Reacts on changed layer paramters.

void dataToWidget	(	DoubleReal	x,
		DoubleReal	y,
		QPoint &	point,
		bool	flipped = `false`,
		bool	percentage = `false`
	)

Calls SpectrumCanvas::dataToWidget_(), takes mirror mode into account.

void dataToWidget	(	const PeakType &	peak,
		QPoint &	point,
		bool	flipped = `false`,
		bool	percentage = `true`
	)

For convenience - calls dataToWidget.

void drawAlignment ( QPainter & painter )

Draws the alignment on painter.

void drawAnnotations	(	Size	layer_index,
		QPainter &	painter
	)

Draws all annotation items of layer_index on painter.

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

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

void drawDashedLine_	(	const QPoint &	from,
		const QPoint &	to,
		QPainter &	painter
	)			`[protected]`

Draws a dashed line using the highlighted peak color parameter.

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

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

void drawHighlightedPeak_	(	Size	layer_index,
		const PeakIndex &	peak,
		QPainter &	painter,
		bool	draw_elongation = `false`
	)			`[protected]`

Draws a highlighted peak; if draw_elongation is true, the elongation line is drawn (for measuring).

void ensureAnnotationsWithinDataRange_ ( ) [protected]

Ensure that all annotations are within data range.

PeakIndex findPeakAtPosition_ ( QPoint ) [protected]

Find peak next to the given position.

bool finishAdding_ ( ) [protected, virtual]

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

Implements SpectrumCanvas.

void flipLayer ( Size index )

Flips the layer with index up/downwards.

Referenced by TOPPViewBase::layerContextMenu().

bool flippedLayersExist ( )

Returns whether flipped layers exist or not.

Referenced by TOPPViewBase::layerContextMenu().

std::vector<std::pair<Size, Size> > getAlignedPeaksIndices ( )

Returns aligned_peaks_indices_.

DoubleReal getAlignmentScore ( )

Returns the score of the alignment.

Referenced by TOPPViewBase::showSpectrumAlignmentDialog().

Size getAlignmentSize ( )

Returns the number of aligned pairs of peaks.

Referenced by TOPPViewBase::showSpectrumAlignmentDialog().

DrawModes getDrawMode ( ) const

Returns the draw mode of the current layer.

Referenced by TOPPViewBase::updateToolBar().

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.

void keyPressEvent ( QKeyEvent * e ) [protected]

Reimplemented from SpectrumCanvas.

bool mirrorModeActive ( )

Returns whether this widget is currently in mirror mode.

Referenced by TOPPViewBase::showSpectrumAlignmentDialog(), and TOPPViewBase::updateMenu().

void mouseMoveEvent ( QMouseEvent * e ) [protected]

void mousePressEvent ( QMouseEvent * e ) [protected]

void mouseReleaseEvent ( QMouseEvent * e ) [protected]

void paint	(	QPainter *	paint_device,
		QPaintEvent *	e
	)

Actual painting takes place here.

void paintEvent ( QPaintEvent * e ) [protected]

virtual void paintGridLines_ ( QPainter & painter ) [protected, virtual]

Helper function to paint grid lines.

Reimplemented from SpectrumCanvas.

void performAlignment	(	Size	layer_index_1,
		Size	layer_index_2,
		const Param &	param
	)

----- Alignment

Performs an alignment of the layers with layer_index_1 and layer_index_2

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.

void resetAlignment ( )

Resets alignment_.

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.

void setCurrentLayerPeakPenStyle ( Qt::PenStyle ps )

Set's the Qt PenStyle of the active layer.

void setDrawMode ( DrawModes mode )

Sets draw mode of the current layer.

Referenced by TOPPViewBase::setDrawMode1D().

void setMirrorModeActive ( bool b )

Sets whether this widget is currently in mirror mode.

Referenced by TOPPViewBase::layerContextMenu().

void setSwappedAxis ( bool swapped )

is the widget shown vertically? (for projections)

void setVisibleArea ( DRange< 2 > range ) [slot]

Sets the visible area.

Sets the visible area to a new value. Note that it does not emit visibleAreaChanged()

Parameters:

range

the new visible area

Reimplemented from SpectrumCanvas.

Referenced by IDEvaluationBase::setVisibleArea().

virtual void showCurrentLayerPreferences ( ) [virtual]

Shows the preferences dialog of the active layer.

Implements SpectrumCanvas.

void showCurrentPeaksAs2D ( ) [signal]

Requests to display all spectra in 2D plot.

void showCurrentPeaksAs3D ( ) [signal]

Requests to display all spectra in 3D plot.

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 updateLayer ( Size i ) [virtual, slot]

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

Implements SpectrumCanvas.

void updatePercentageFactor_ ( Size layer_index ) [protected]

Recalculates the current scale factor based on the specified layer (= 1.0 if intensity mode != IM_PERCENTAGE).

virtual void updateScrollbars_ ( ) [protected, virtual]

Updates the scroll bars.

Updates the scrollbars after a change of the visible area.

Reimplemented from SpectrumCanvas.

PointType widgetToData	(	DoubleReal	x,
		DoubleReal	y,
		bool	percentage = `false`
	)

Calls SpectrumCanvas::widgetToData_(), takes mirror mode into account.

PointType widgetToData	(	const QPoint &	pos,
		bool	percentage = `false`
	)

For convenience - calls widgetToData.

virtual void zoomForward_ ( ) [protected, virtual]

Go forward in zoom history.

Reimplemented from SpectrumCanvas.

Member Data Documentation

std::vector<std::pair<Size, Size> > aligned_peaks_indices_ [protected]

Stores the peak indizes of pairs of aligned peaks in both spectra.

std::vector<std::pair<DoubleReal, DoubleReal> > aligned_peaks_mz_delta_ [protected]

Stores the alignment as MZ values of pairs of aligned peaks in both spectra.

Size alignment_layer_1_ [protected]

Layer index of the first alignment layer.

Size alignment_layer_2_ [protected]

Layer index of the second alignment layer.

DoubleReal alignment_score_ [protected]

Stores the score of the last alignment.

std::vector<DrawModes> draw_modes_ [protected]

Draw modes (for each spectrum).

bool is_swapped_ [protected]

is this widget showing data with swapped m/z and RT axis? (for drawCoordinates_ only)

QPoint measurement_start_point_ [protected]

start point of "ruler" for measure mode

bool mirror_mode_ [protected]

Indicates whether this widget is currently in mirror mode.

bool moving_annotations_ [protected]

Indicates whether annotation items are just being moved on the canvas.

std::vector<Qt::PenStyle> peak_penstyle_ [protected]

Draw style.

bool show_alignment_ [protected]

Indicates whether an alignment is currently visualized.

OpenMS / TOPP release 1.10.0

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

Spectrum1DCanvas Class Reference [Spectrum visualizaion widgets]

Public Types

Public Slots

Signals

Public Member Functions

Protected Slots

Protected Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

Spectrum1DCanvas Class Reference
[Spectrum visualizaion widgets]