Base class for visualization canvas classes. More...

#include <OpenMS/VISUAL/SpectrumCanvas.h>

Inheritance diagram for SpectrumCanvas:

Public Types
Type definitions

enum	ActionModes { AM_TRANSLATE, AM_ZOOM, AM_MEASURE }
	Mouse action modes. More...
enum	IntensityModes { IM_NONE, IM_PERCENTAGE, IM_SNAP, IM_LOG }
	Display modes of intensity. More...
typedef LayerData::ExperimentType	ExperimentType
	Main data type (experiment).
typedef LayerData::ExperimentSharedPtrType	ExperimentSharedPtrType
	Main managed data type (experiment).
typedef LayerData::FeatureMapType	FeatureMapType
	Main data type (features).
typedef LayerData::FeatureMapSharedPtrType	FeatureMapSharedPtrType
	Main managed data type (features).
typedef LayerData::ConsensusMapType	ConsensusMapType
	Main data type (consensus features).
typedef LayerData::ConsensusMapSharedPtrType	ConsensusMapSharedPtrType
	Main managed data type (consensus features).
typedef ExperimentType::SpectrumType	SpectrumType
	Spectrum type.
typedef SpectrumType::ConstIterator	SpectrumConstIteratorType
	Spectrum iterator type (iterates over peaks).
typedef SpectrumType::PeakType	PeakType
	Peak type.
typedef FeatureMapType::FeatureType	FeatureType
	Feature type.
typedef DPosition< 2 >	PointType
	Type of the Points.
typedef DRange< 2 >	AreaType
	Types of Ranges/Areas.
Public Slots
void	changeVisibility (Size i, bool b)
	change the visibility of a layer
void	changeLayerFilterState (Size i, bool b)
	change if the defined data filters are used
void	showGridLines (bool show)
	Whether or not to show grid lines.
void	resetZoom (bool repaint=true)
	Zooms fully out and resets the zoom stack.
void	setVisibleArea (AreaType area)
	Sets the visible area.
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	setAdditionalContextMenu (QMenu *menu)
	Sets the additional context menu. If not 0, this menu is added to the context menu of the canvas.
void	getVisiblePeakData (ExperimentType &map) const
	Fills the handed over `map` with the visible peaks of the current layer.
void	getVisibleFeatureData (FeatureMapType &map) const
	Fills the handed over `map` with the visible features of the current layer.
void	getVisibleConsensusData (ConsensusMapType &map) const
	Fills the handed over `map` with the visible consensus features of the current layer.
void	getVisibleIdentifications (std::vector< PeptideIdentification > &peptides) const
	Fills the handed over `peptides` with the visible peptide identifications of the current layer.
virtual void	updateLayer (Size i)=0
	Updates layer `i` when the data in the corresponding file changes.
Signals
void	layerModficationChange (Size layer, bool modified)
	Signal emitted whenever the modification status of a layer changes (editing and storing).
void	layerActivated (QWidget *w)
	Signal emitted whenever a new layer is activated within the current window.
void	layerZoomChanged (QWidget *w)
	Signal emitted whenever the zoom changed.
void	visibleAreaChanged (DRange< 2 > area)
	Change of the visible area.
void	sendCursorStatus (double mz=-1.0, double rt=-1.0)
	Emitted when the cursor position changes (for displaying e.g. in status bar).
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.
void	recalculateAxes ()
	Forces recalculation of axis ticks in the connected widget.
void	updateVScrollbar (float, float, float, float)
	Triggers the update of the vertical scrollbar.
void	updateHScrollbar (float, float, float, float)
	Triggers the update of the horizontal scrollbar.
void	changeLegendVisibility ()
	Toggle axis legend visibility change.
void	actionModeChange ()
	Emitted when the action mode changes.
void	preferencesChange ()
	Emitted when the layer preferences have changed.
Public Member Functions
	SpectrumCanvas (const Param &preferences, QWidget *parent=0)
	Default constructor.
virtual	~SpectrumCanvas ()
	Destructor.
void	setSpectrumWidget (SpectrumWidget *widget)
	Sets the spectrum widget.
SpectrumWidget *	getSpectrumWidget () const
	Returns the spectrum widget.
Int	getActionMode () const
	Returns the action mode.
Int	getIntensityMode () const
	Returns the intensity mode.
void	setIntensityMode (IntensityModes mod)
	Sets the intensity mode.
bool	gridLinesShown () const
	Returns if the grid is currently shown.
const LayerData &	getLayer (Size index) const
	returns the layer data with index `index`
const LayerData &	getCurrentLayer () const
	returns the layer data of the active layer
LayerData &	getCurrentLayer ()
	returns the layer data of the active layer
bool	getLayerFlag (LayerData::Flags f) const
	returns a layer flag of the current layer
void	setLayerFlag (LayerData::Flags f, bool value)
	sets a layer flag of the current layer
bool	getLayerFlag (Size layer, LayerData::Flags f) const
	returns a layer flag of the layer `layer`
void	setLayerFlag (Size layer, LayerData::Flags f, bool value)
	sets a layer flag of the layer `layer`
void	setLabel (LayerData::LabelType label)
const AreaType &	getVisibleArea () const
	Returns the currently visible area.
virtual void	setFilters (const DataFilters &filters)
	Sets the filters applied to the data before drawing (for the current layer).
bool	isMzToXAxis ()
	Returns the mapping of m/z to axes.
void	mzToXAxis (bool mz_to_x_axis)
	Sets the mapping of m/z to axes.
bool	addLayer (std::vector< PeptideIdentification > &peptides, const String &filename="")
	Add an identification data layer.
Real	getCurrentMinIntensity () const
	Returns the minimum intensity of the active layer.
Real	getCurrentMaxIntensity () const
	Returns the maximum intensity of the active layer.
Real	getMinIntensity (Size index) const
	Returns the minimum intensity of the layer with index `index`.
Real	getMaxIntensity (Size index) const
	Returns the maximum intensity of the layer with index `index`.
void	setLayerName (Size i, const String &name)
	Sets the `name` of layer `i`.
String	getLayerName (Size i)
	Gets the name of layer `i`.
void	setCurrentLayerParameters (const Param &param)
	Sets the parameters of the current layer.
const DRange< 3 > &	getDataRange ()
	Returns the area which encloses all data points.
DoubleReal	getSnapFactor ()
	Returns the first intensity scaling factor for 'snap to maximum intensity mode'.
DoubleReal	getPercentageFactor ()
	Returns the percentage factor.
virtual void	showCurrentLayerPreferences ()=0
	Shows the preferences dialog of the active layer.
virtual void	showMetaData (bool modifiable=false, Int index=-1)
	Shows a dialog with the meta data.
virtual void	saveCurrentLayer (bool visible)=0
	Saves the current layer data.
Dataset handling methods
See also: changeVisibility
Size	getLayerCount () const
	Returns the number of layers.
Size	activeLayerIndex () const
	Returns the index of the active layer.
virtual void	activateLayer (Size layer_index)=0
	change the active layer (the one that is used for selecting and so on)
virtual void	removeLayer (Size layer_index)=0
	removes the layer with index `layer_index`
bool	addLayer (ExperimentSharedPtrType map, const String &filename="")
	Add a peak data layer.
bool	addLayer (FeatureMapSharedPtrType map, const String &filename="")
	Add a feature data layer.
bool	addLayer (ConsensusMapSharedPtrType map, const String &filename="")
	Add a consensus feature data layer.
Protected Slots
void	updateCursor_ ()
	Updates the cursor accoring to the current action mode.
Protected Member Functions
void	drawText_ (QPainter &painter, QStringList text)
	Draws several lines of text to the upper right corner of the widget.
DoubleReal	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).
virtual bool	finishAdding_ ()=0
	Method that is called when a new layer has been added.
LayerData &	getLayer_ (Size index)
	Returns the layer with index `index`.
LayerData &	getCurrentLayer_ ()
	Returns the currently active layer.
ExperimentSharedPtrType	currentPeakData_ ()
	Returns the currently active layer (mutable).
virtual void	intensityModeChange_ ()
	This method is called whenever the intensity mode changes. Reimplement if you need to react on such changes.
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.
PointType	widgetToData_ (DoubleReal x, DoubleReal y)
	Convert widget to chart coordinates.
PointType	widgetToData_ (const QPoint &pos)
	Calls widgetToData_ with x and y position of `pos`.
void	dataToWidget_ (DoubleReal x, DoubleReal y, QPoint &point)
	Convert chart to widget coordinates.
virtual void	paintGridLines_ (QPainter &painter)
	Helper function to paint grid lines.
void	recalculateRanges_ (UInt mz_dim, UInt rt_dim, UInt it_dim)
	Recalculates the overall_data_range_.
virtual void	update_ (const char *caller_name)
	Updates the diplayed data.
void	modificationStatus_ (Size layer_index, bool modified)
	Takes all actions necessary when the modification status of a layer changes (signals etc.).
void	adjustBuffer_ ()
	Changes the size of the paint buffer to the currently required size.
template<typename PeakType >
void	addDataProcessing_ (MSExperiment< PeakType > &map, DataProcessing::ProcessingAction action) const
	Data processing setter for peak maps.
reimplemented QT events

void	resizeEvent (QResizeEvent *e)
void	wheelEvent (QWheelEvent *e)
void	keyPressEvent (QKeyEvent *e)
void	keyReleaseEvent (QKeyEvent *e)
void	focusOutEvent (QFocusEvent *e)
void	leaveEvent (QEvent *e)
void	enterEvent (QEvent *e)
Zoom stack methods

void	zoom (int x, int y, bool zoom_in)
	Zooms such that screen point x, y would still point to the same data point.
void	zoomBack_ ()
	Go backward in zoom history.
virtual void	zoomForward_ ()
	Go forward in zoom history.
void	zoomAdd_ (const AreaType &area)
	Add a visible area to the zoom stack.
void	zoomClear_ ()
	Clears the zoom stack and invalidates the current zoom position. After calling this, a valid zoom position has to be added immediately.
Translation methods, which are called when cursor buttons are pressed

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.
Protected Attributes
QImage	buffer_
	Buffer that stores the actual peak information.
ActionModes	action_mode_
	Stores the current action mode (Pick, Zoom, Translate).
IntensityModes	intensity_mode_
	Stores the used intensity mode function.
std::vector< LayerData >	layers_
	Layer data.
bool	mz_to_x_axis_
	Stores the mapping of m/z.
AreaType	visible_area_
	Stores the currently visible area.
DRange< 3 >	overall_data_range_
	Stores the data range (m/z, RT and intensity) of all layers.
bool	show_grid_
	Stores whether or not to show a grid.
std::vector< AreaType >	zoom_stack_
	The zoom stack.
std::vector< AreaType >::iterator	zoom_pos_
	The current position in the zoom stack.
bool	update_buffer_
	Whether to recalculate the data in the buffer when repainting.
Size	current_layer_
	Stores the index of the currently active layer.
SpectrumWidget *	spectrum_widget_
	Back-pointer to the enclosing spectrum widget.
QPoint	last_mouse_pos_
	start position of mouse actions
double	percentage_factor_
	Intensity scaling factor for relative scale with multiple layers.
std::vector< DoubleReal >	snap_factors_
	Intensity scaling factor for 'snap to maximum intensity mode'.
QRubberBand	rubber_band_
	Rubber band for selected area.
QMenu *	context_add_
	External context menu extension.
bool	show_timing_
	Flag that determines if timimg data is printed to the command line.
PeakIndex	selected_peak_
	selected peak
PeakIndex	measurement_start_
	start peak of measuring mode

Detailed Description

Base class for visualization canvas classes.

This class is the base class for the spectrum data views.

It also provides commonly used constants such as ActionModes or IntensityModes.

To provide additional spectrum views, you can derive from this class. You should also create a subclass from SpectrumWidget which encloses your class derived from SpectrumCanvas. To integrate your class into TOPPView, you also need to derive a class from SpectrumWidget.

All derived classes should follow these interface conventions:

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

Measure mode

Activated using the SHIFT key

Improvement:: Add log mode (Hiwi)

Todo:: Allow reordering the layer list by drag-and-drop (Hiwi, Johannes)

Member Typedef Documentation

typedef DRange<2> AreaType

Types of Ranges/Areas.

typedef LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType

Main managed data type (consensus features).

typedef LayerData::ConsensusMapType ConsensusMapType

Main data type (consensus features).

typedef LayerData::ExperimentSharedPtrType ExperimentSharedPtrType

Main managed data type (experiment).

typedef LayerData::ExperimentType ExperimentType

Main data type (experiment).

typedef LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType

Main managed data type (features).

typedef LayerData::FeatureMapType FeatureMapType

Main data type (features).

typedef FeatureMapType::FeatureType FeatureType

Feature type.

typedef SpectrumType::PeakType PeakType

Peak type.

typedef DPosition<2> PointType

Type of the Points.

typedef SpectrumType::ConstIterator SpectrumConstIteratorType

Spectrum iterator type (iterates over peaks).

typedef ExperimentType::SpectrumType SpectrumType

Spectrum type.

Member Enumeration Documentation

enum ActionModes

Mouse action modes.

Enumerator:

AM_TRANSLATE	translate
AM_ZOOM	zoom
AM_MEASURE	measure

enum IntensityModes

Display modes of intensity.

Enumerator:

IM_NONE	Normal mode: f(x)=x.
IM_PERCENTAGE	Shows intensities normalized by layer maximum: f(x)=x/max(x)*100.
IM_SNAP	Shows the maximum displayed intensity as if it was the overall maximum intensity.
IM_LOG	Logarithmic mode.

Constructor & Destructor Documentation

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

Default constructor.

virtual ~SpectrumCanvas ( ) [virtual]

Destructor.

Member Function Documentation

void actionModeChange ( ) [signal]

Emitted when the action mode changes.

virtual void activateLayer ( Size layer_index ) [pure virtual]

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

Implemented in Spectrum1DCanvas, Spectrum2DCanvas, and Spectrum3DCanvas.

Referenced by TOPPViewBase::layerSelectionChange().

Size activeLayerIndex ( ) const

Returns the index of the active layer.

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

void addDataProcessing_	(	MSExperiment< PeakType > &	map,
		DataProcessing::ProcessingAction	action
	)			const `[inline, protected]`

Data processing setter for peak maps.

References DataProcessing::getSoftware(), VersionInfo::getVersion(), DateTime::now(), DataProcessing::setCompletionTime(), Software::setName(), DataProcessing::setProcessingActions(), and Software::setVersion().

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

Add a peak data layer.

If chromatograms are present, a chromatogram layer is shown. Otherwise a peak layer is shown. Make sure to remove chromatograms from peak data and vice versa.

Parameters:

	map	Shared Pointer to input map. It can be performed in constant time and does not double the required memory.
	filename	This absolute filename is used to monitor changes in the file and reload the data

Returns:: If a new layer was created

Referenced by TOPPViewBase::addData(), IDEvaluationBase::addSearchFile(), TOPPViewBase::showCurrentPeaksAs2D(), and TOPPViewBase::showCurrentPeaksAs3D().

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

Add a consensus feature data layer.

Parameters:

	map	Shared Pointer to input map. It can be performed in constant time and does not double the required memory.
	filename	This absolute filename is used to monitor changes in the file and reload the data

Returns:: If a new layer was created

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

Add an identification data layer.

Parameters:

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

Returns:: If a new layer was created

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

Add a feature data layer.

Parameters:

	map	Shared Pointer to input map. It can be performed in constant time and does not double the required memory.
	filename	This absolute filename is used to monitor changes in the file and reload the data

Returns:: If a new layer was created

void adjustBuffer_ ( ) [protected]

Changes the size of the paint buffer to the currently required size.

void changeLayerFilterState	(	Size	i,
		bool	b
	)			`[slot]`

change if the defined data filters are used

Parameters:

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

Referenced by TOPPViewBase::layerFilterVisibilityChange().

void changeLegendVisibility ( ) [signal]

Toggle axis legend visibility change.

void changeVisibility	(	Size	i,
		bool	b
	)			`[slot]`

change the visibility of a layer

Parameters:

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

Referenced by TOPPViewBase::layerVisibilityChange().

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

Reimplemented in Spectrum1DCanvas.

ExperimentSharedPtrType currentPeakData_ ( ) [inline, protected]

Returns the currently active layer (mutable).

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 in Spectrum2DCanvas.

References SpectrumCanvas::IM_LOG.

void drawText_	(	QPainter &	painter,
		QStringList	text
	)			`[protected]`

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

void enterEvent ( QEvent * e ) [protected]

virtual bool finishAdding_ ( ) [protected, pure virtual]

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

Implemented in Spectrum1DCanvas, Spectrum2DCanvas, and Spectrum3DCanvas.

void focusOutEvent ( QFocusEvent * e ) [protected]

Int getActionMode ( ) const [inline]

Returns the action mode.

Returns the current action mode of type ActionModes

Returns:: the current action mode

LayerData& getCurrentLayer ( ) [inline]

returns the layer data of the active layer

References OPENMS_PRECONDITION.

const LayerData& getCurrentLayer ( ) const [inline]

LayerData& getCurrentLayer_ ( ) [inline, protected]

Returns the currently active layer.

Real getCurrentMaxIntensity ( ) const [inline]

Returns the maximum intensity of the active layer.

References LayerData::DT_CHROMATOGRAM, LayerData::DT_FEATURE, and LayerData::DT_PEAK.

Real getCurrentMinIntensity ( ) const [inline]

Returns the minimum intensity of the active layer.

References LayerData::DT_CHROMATOGRAM, LayerData::DT_FEATURE, and LayerData::DT_PEAK.

const DRange<3>& getDataRange ( )

Returns the area which encloses all data points.

See also:: overall_data_range_

DoubleReal getIdentificationMZ_	(	const Size	layer_index,
		const PeptideIdentification &	peptide
	)			const `[protected]`

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

Int getIntensityMode ( ) const [inline]

Returns the intensity mode.

Returns the current intensity mode of type IntensityModes

Returns:: the current intensity mode

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

const LayerData& getLayer ( Size index ) const [inline]

returns the layer data with index index

References OPENMS_PRECONDITION.

Referenced by TOPPViewBase::addData(), TOPPViewBase::fileChanged_(), TOPPViewBase::getFilenamesOfOpenFiles_(), TOPPViewBase::layerContextMenu(), TOPPViewBase::layerVisibilityChange(), and TOPPViewBase::updateLayerBar().

LayerData& getLayer_ ( Size index ) [inline, protected]

Returns the layer with index index.

References OPENMS_PRECONDITION.

Size getLayerCount ( ) const [inline]

Returns the number of layers.

Referenced by TOPPViewBase::addData(), IDEvaluationBase::addSearchFile(), TOPPViewBase::enhancedWorkspaceWindowChanged(), TOPPViewBase::fileChanged_(), TOPPViewBase::getFilenamesOfOpenFiles_(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), and TOPPViewBase::updateToolBar().

bool getLayerFlag ( LayerData::Flags f ) const [inline]

returns a layer flag of the current layer

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

bool getLayerFlag	(	Size	layer,
		LayerData::Flags	f
	)			const `[inline]`

returns a layer flag of the layer layer

References OPENMS_PRECONDITION.

String getLayerName ( Size i )

Gets the name of layer i.

Real getMaxIntensity ( Size index ) const [inline]

Returns the maximum intensity of the layer with index index.

References LayerData::DT_CHROMATOGRAM, LayerData::DT_FEATURE, and LayerData::DT_PEAK.

Real getMinIntensity ( Size index ) const [inline]

Returns the minimum intensity of the layer with index index.

References LayerData::DT_CHROMATOGRAM, LayerData::DT_FEATURE, and LayerData::DT_PEAK.

DoubleReal getPercentageFactor ( )

Returns the percentage factor.

DoubleReal getSnapFactor ( )

Returns the first intensity scaling factor for 'snap to maximum intensity mode'.

See also:: snap_factors_

SpectrumWidget* getSpectrumWidget ( ) const [inline]

Returns the spectrum widget.

Returns the enclosing spectrum widget

Returns:: the spectrum widget

const AreaType& getVisibleArea ( ) const [inline]

Returns the currently visible area.

See also:: visible_area_

Referenced by TOPPViewBase::layerZoomChanged().

void getVisibleConsensusData ( ConsensusMapType & map ) const [slot]

Fills the handed over map with the visible consensus features of the current layer.

Takes zoom area and data filters into account.

If the current layer is not a consensus feature layer, map is cleared only.

Referenced by TOPPViewBase::runTOPPTool_().

void getVisibleFeatureData ( FeatureMapType & map ) const [slot]

Fills the handed over map with the visible features of the current layer.

Takes zoom area and data filters into account.

If the current layer is not a feature layer, map is cleared only.

Referenced by TOPPViewBase::runTOPPTool_().

void getVisibleIdentifications ( std::vector< PeptideIdentification > & peptides ) const [slot]

Fills the handed over peptides with the visible peptide identifications of the current layer.

Takes zoom area into account.

If the current layer is not an identification data layer, peptides is cleared only.

void getVisiblePeakData ( ExperimentType & map ) const [slot]

Fills the handed over map with the visible peaks of the current layer.

Takes zoom area and data filters into account.

If the current layer is not a peak layer, map is cleared only.

Referenced by TOPPViewBase::runTOPPTool_().

bool gridLinesShown ( ) const [inline]

Returns if the grid is currently shown.

Returns:: true if the grid is visible, false otherwise

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 in Spectrum1DCanvas, and Spectrum2DCanvas.

virtual void intensityModeChange_ ( ) [protected, virtual]

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

Reimplemented in Spectrum1DCanvas, and Spectrum2DCanvas.

bool isMzToXAxis ( ) [inline]

Returns the mapping of m/z to axes.

void keyPressEvent ( QKeyEvent * e ) [protected]

Reimplemented in Spectrum1DCanvas, and Spectrum2DCanvas.

void keyReleaseEvent ( QKeyEvent * e ) [protected]

Reimplemented in Spectrum2DCanvas.

void layerActivated ( QWidget * w ) [signal]

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

void layerModficationChange	(	Size	layer,
		bool	modified
	)			`[signal]`

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

void layerZoomChanged ( QWidget * w ) [signal]

Signal emitted whenever the zoom changed.

void leaveEvent ( QEvent * e ) [protected]

void modificationStatus_	(	Size	layer_index,
		bool	modified
	)			`[protected]`

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

void mzToXAxis ( bool mz_to_x_axis )

Sets the mapping of m/z to axes.

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

Helper function to paint grid lines.

Reimplemented in Spectrum1DCanvas.

void preferencesChange ( ) [signal]

Emitted when the layer preferences have changed.

void recalculateAxes ( ) [signal]

Forces recalculation of axis ticks in the connected widget.

void recalculateRanges_	(	UInt	mz_dim,
		UInt	rt_dim,
		UInt	it_dim
	)			`[protected]`

Recalculates the overall_data_range_.

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

Parameters:

	mz_dim	Int of m/z in overall_data_range_
	rt_dim	Int of RT in overall_data_range_
	it_dim	Int of intensity in overall_data_range_

virtual void recalculateSnapFactor_ ( ) [protected, virtual]

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

See also:: snap_factors_

Reimplemented in Spectrum1DCanvas, and Spectrum2DCanvas.

virtual void removeLayer ( Size layer_index ) [pure virtual]

removes the layer with index layer_index

Implemented in Spectrum1DCanvas, Spectrum2DCanvas, and Spectrum3DCanvas.

Referenced by TOPPViewBase::layerContextMenu().

void resetZoom ( bool repaint = true ) [slot]

Zooms fully out and resets the zoom stack.

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

Parameters:

repaint

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

Referenced by TOPPViewBase::resetZoom(), and IDEvaluationBase::resetZoom().

void resizeEvent ( QResizeEvent * e ) [protected]

Reimplemented in Spectrum3DCanvas.

virtual void saveCurrentLayer ( bool visible ) [pure virtual]

Saves the current layer data.

Parameters:

visible

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

Implemented in Spectrum1DCanvas, Spectrum2DCanvas, and Spectrum3DCanvas.

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

void sendCursorStatus	(	double	mz = `-1.0`,
		double	rt = `-1.0`
	)			`[signal]`

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

void sendStatusMessage	(	std::string	message,
		OpenMS::UInt	time
	)			`[signal]`

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

void setAdditionalContextMenu ( QMenu * menu ) [slot]

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

void setCurrentLayerParameters ( const Param & param ) [inline]

Sets the parameters of the current layer.

Referenced by TOPPViewBase::loadFiles().

virtual void setFilters ( const DataFilters & filters ) [virtual]

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

Referenced by TOPPViewBase::addData(), TOPPViewBase::filterContextMenu(), and TOPPViewBase::filterEdit().

void setIntensityMode ( IntensityModes mod ) [inline]

Sets the intensity mode.

Sets the intensity mode

Parameters:

mod

the new intensity mode

See also:: intensityModeChange_()

void setLabel ( LayerData::LabelType label ) [inline]

References OPENMS_PRECONDITION.

Referenced by TOPPViewBase::changeLabel().

void setLayerFlag	(	LayerData::Flags	f,
		bool	value
	)			`[inline]`

sets a layer flag of the current layer

Referenced by TOPPViewBase::changeUnassigned().

void setLayerFlag	(	Size	layer,
		LayerData::Flags	f,
		bool	value
	)			`[inline]`

sets a layer flag of the layer layer

References OPENMS_PRECONDITION.

void setLayerName	(	Size	i,
		const String &	name
	)

Sets the name of layer i.

Referenced by TOPPViewBase::addData(), IDEvaluationBase::addSearchFile(), TOPPViewBase::layerContextMenu(), TOPPViewBase::showCurrentPeaksAs2D(), and TOPPViewBase::showCurrentPeaksAs3D().

void setSpectrumWidget ( SpectrumWidget * widget ) [inline]

Sets the spectrum widget.

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

Parameters:

widget

the spectrum widget

void setVisibleArea ( AreaType area ) [slot]

Sets the visible area.

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

Parameters:

area

the new visible area

Reimplemented in Spectrum1DCanvas.

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

virtual void showCurrentLayerPreferences ( ) [pure virtual]

Shows the preferences dialog of the active layer.

Implemented in Spectrum1DCanvas, Spectrum2DCanvas, and Spectrum3DCanvas.

Referenced by TOPPViewBase::layerContextMenu(), TOPPViewBase::layerEdit(), and TOPPViewBase::showPreferences().

void showGridLines ( bool show ) [slot]

Whether or not to show grid lines.

Sets whether grid lines are shown or not.

Parameters:

show

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

Referenced by TOPPViewBase::toggleGridLines().

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

Shows a dialog with the meta data.

Parameters:

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

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

virtual void translateBackward_ ( ) [protected, virtual]

Translation bound to the 'Down' key.

Reimplemented in Spectrum2DCanvas, and Spectrum3DCanvas.

virtual void translateForward_ ( ) [protected, virtual]

Translation bound to the 'Up' key.

Reimplemented in Spectrum2DCanvas, and Spectrum3DCanvas.

virtual void translateLeft_ ( ) [protected, virtual]

Translation bound to the 'Left' key.

Reimplemented in Spectrum1DCanvas, Spectrum2DCanvas, and Spectrum3DCanvas.

virtual void translateRight_ ( ) [protected, virtual]

Translation bound to the 'Rightt' key.

Reimplemented in Spectrum1DCanvas, Spectrum2DCanvas, and Spectrum3DCanvas.

virtual void update_ ( const char * caller_name ) [protected, virtual]

Updates the diplayed 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 __PRETTY_FUNCTION__).

Reimplemented in Spectrum3DCanvas.

void updateCursor_ ( ) [protected, slot]

Updates the cursor accoring to the current action mode.

void updateHScrollbar	(	float	,
		float	,
		float	,
		float
	)			`[signal]`

Triggers the update of the horizontal scrollbar.

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

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

Implemented in Spectrum1DCanvas, Spectrum2DCanvas, and Spectrum3DCanvas.

Referenced by TOPPViewBase::fileChanged_().

virtual void updateScrollbars_ ( ) [protected, virtual]

Updates the scroll bars.

Updates the scrollbars after a change of the visible area.

Reimplemented in Spectrum1DCanvas, and Spectrum2DCanvas.

void updateVScrollbar	(	float	,
		float	,
		float	,
		float
	)			`[signal]`

Triggers the update of the vertical scrollbar.

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 in Spectrum2DCanvas.

void visibleAreaChanged ( DRange< 2 > area ) [signal]

Change of the visible area.

Signal emitted whenever the visible area changes.

Parameters:

area

The new visible area.

void wheelEvent ( QWheelEvent * e ) [protected]

PointType widgetToData_ ( const QPoint & pos ) [inline, protected]

Calls widgetToData_ with x and y position of pos.

PointType widgetToData_	(	DoubleReal	x,
		DoubleReal	y
	)			`[inline, protected]`

Convert widget to chart coordinates.

Translates widget coordinates to chart coordinates.

Parameters:

	x	the widget coordinate x
	y	the widget coordinate y

Returns:: chart coordinates

void zoom	(	int	x,
		int	y,
		bool	zoom_in
	)			`[protected]`

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

void zoomAdd_ ( const AreaType & area ) [protected]

Add a visible area to the zoom stack.

void zoomBack_ ( ) [protected]

Go backward in zoom history.

void zoomClear_ ( ) [protected]

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

virtual void zoomForward_ ( ) [protected, virtual]

Go forward in zoom history.

Reimplemented in Spectrum1DCanvas.

Member Data Documentation

ActionModes action_mode_ [protected]

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

QImage buffer_ [protected]

Buffer that stores the actual peak information.

QMenu* context_add_ [protected]

External context menu extension.

Size current_layer_ [protected]

Stores the index of the currently active layer.

IntensityModes intensity_mode_ [protected]

Stores the used intensity mode function.

QPoint last_mouse_pos_ [protected]

start position of mouse actions

std::vector<LayerData> layers_ [protected]

Layer data.

PeakIndex measurement_start_ [protected]

start peak of measuring mode

Reimplemented in Spectrum2DCanvas.

bool mz_to_x_axis_ [protected]

Stores the mapping of m/z.

DRange<3> overall_data_range_ [protected]

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

Dimension 0 is the m/z dimension.
Dimension 1 is the RT dimension (2D and 3D view) or the intensity dimension (1D view).
Dimension 2 is the intensity dimension (2D and 3D view) or the RT dimension (1D view).

double percentage_factor_ [protected]

Intensity scaling factor for relative scale with multiple layers.

In this mode all layers are scaled to the same maximum.

QRubberBand rubber_band_ [protected]

Rubber band for selected area.

PeakIndex selected_peak_ [protected]

selected peak

Reimplemented in Spectrum2DCanvas.

bool show_grid_ [protected]

Stores whether or not to show a grid.

bool show_timing_ [protected]

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

std::vector<DoubleReal> snap_factors_ [protected]

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

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

SpectrumWidget* spectrum_widget_ [protected]

Back-pointer to the enclosing spectrum widget.

bool update_buffer_ [protected]

Whether to recalculate the data in the buffer when repainting.

AreaType visible_area_ [protected]

Stores the currently visible area.

Dimension 0 is the m/z dimension.
Dimension 1 is the RT dimension (2D and 3D view) or the intensity dimension (1D view).

std::vector<AreaType>::iterator zoom_pos_ [protected]

The current position in the zoom stack.

std::vector<AreaType> zoom_stack_ [protected]

The zoom stack.

OpenMS / TOPP release 1.10.0

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

SpectrumCanvas Class Reference [Spectrum visualizaion widgets]

Public Types

Public Slots

Signals

Public Member Functions

Protected Slots

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

SpectrumCanvas Class Reference
[Spectrum visualizaion widgets]