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) More...

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

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 Slots
void	changeVisibility (Size i, bool b)
	change the visibility of a layer More...

void	changeLayerFilterState (Size i, bool b)
	change if the defined data filters are used More...

void	showGridLines (bool show)
	Whether or not to show grid lines. More...

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

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

virtual void	horizontalScrollBarChange (int value)
	Notifies the canvas that the horizontal scrollbar has been moved. More...

virtual void	verticalScrollBarChange (int value)
	Notifies the canvas that the vertical scrollbar has been moved. More...

void	setAdditionalContextMenu (QMenu *menu)
	Sets the additional context menu. If not 0, this menu is added to the context menu of the canvas. More...

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

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

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

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

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

Signals
void	layerModficationChange (Size layer, bool modified)
	Signal emitted whenever the modification status of a layer changes (editing and storing) More...

void	layerActivated (QWidget *w)
	Signal emitted whenever a new layer is activated within the current window. More...

void	layerZoomChanged (QWidget *w)
	Signal emitted whenever the zoom changed. More...

void	visibleAreaChanged (DRange< 2 > area)
	Change of the visible area. More...

void	sendCursorStatus (double mz=-1.0, double rt=-1.0)
	Emitted when the cursor position changes (for displaying e.g. in status bar) More...

void	sendStatusMessage (std::string message, OpenMS::UInt time)
	Emits a status message that should be displayed for `time` ms. If `time` is 0 the message should be displayed until the next message is emitted. More...

void	recalculateAxes ()
	Forces recalculation of axis ticks in the connected widget. More...

void	updateVScrollbar (float, float, float, float)
	Triggers the update of the vertical scrollbar. More...

void	updateHScrollbar (float, float, float, float)
	Triggers the update of the horizontal scrollbar. More...

void	changeLegendVisibility ()
	Toggle axis legend visibility change. More...

void	actionModeChange ()
	Emitted when the action mode changes. More...

void	preferencesChange ()
	Emitted when the layer preferences have changed. More...

Public Member Functions
	SpectrumCanvas (const Param &preferences, QWidget *parent=0)
	Default constructor. More...

virtual	~SpectrumCanvas ()
	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...

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	showCurrentLayerPreferences ()=0
	Shows the preferences dialog of the active layer. More...

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

virtual void	saveCurrentLayer (bool visible)=0
	Saves the current layer data. More...

Dataset handling methods
See also changeVisibility
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, 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...

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

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

Protected Member Functions
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...

virtual bool	finishAdding_ ()=0
	Method that is called when a new layer has been added. More...

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

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

ExperimentSharedPtrType	currentPeakData_ ()
	Returns the currently active layer (mutable) More...

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	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...

virtual void	update_ (const char *caller_name)
	Updates the displayed data. More...

void	modificationStatus_ (Size layer_index, bool modified)
	Takes all actions necessary when the modification status of a layer changes (signals etc.) More...

void	adjustBuffer_ ()
	Changes the size of the paint buffer to the currently required size. More...

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

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
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...

Translation methods, which are called when cursor buttons are pressed
virtual void	translateLeft_ (Qt::KeyboardModifiers m)
	Translation bound to the 'Left' key. More...

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

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

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

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

◆ AreaType

typedef DRange<2> AreaType

Types of Ranges/Areas.

◆ ConsensusMapSharedPtrType

typedef LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType

Main managed data type (consensus features)

◆ ConsensusMapType

typedef LayerData::ConsensusMapType ConsensusMapType

Main data type (consensus features)

◆ ExperimentSharedPtrType

typedef LayerData::ExperimentSharedPtrType ExperimentSharedPtrType

Main managed data type (experiment)

◆ ExperimentType

typedef LayerData::ExperimentType ExperimentType

Main data type (experiment)

◆ FeatureMapSharedPtrType

typedef LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType

Main managed data type (features)

◆ FeatureMapType

typedef LayerData::FeatureMapType FeatureMapType

Main data type (features)

◆ FeatureType

typedef FeatureMapType::FeatureType FeatureType

Feature type.

◆ PeakType

typedef SpectrumType::PeakType PeakType

Peak type.

◆ PointType

typedef DPosition<2> PointType

Type of the Points.

◆ SpectrumConstIteratorType

typedef SpectrumType::ConstIterator SpectrumConstIteratorType

Spectrum iterator type (iterates over peaks)

◆ SpectrumType

typedef ExperimentType::SpectrumType SpectrumType

Spectrum type.

Member Enumeration Documentation

◆ ActionModes

enum ActionModes

Mouse action modes.

Enumerator
AM_TRANSLATE	translate
AM_ZOOM	zoom
AM_MEASURE	measure

◆ IntensityModes

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()

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

Default constructor.

◆ ~SpectrumCanvas()

virtual ~SpectrumCanvas ( )

virtual

Destructor.

Member Function Documentation

◆ actionModeChange

void actionModeChange ( )

signal

Emitted when the action mode changes.

◆ activateLayer()

virtual void activateLayer ( Size layer_index )

pure virtual

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

Referenced by TOPPViewBase::layerSelectionChange().

◆ activeLayerIndex()

Size activeLayerIndex ( ) const

Returns the index of the active layer.

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

◆ addDataProcessing_()

void addDataProcessing_	(	PeakMap &	map,
		DataProcessing::ProcessingAction	action
	)		const

inlineprotected

Data processing setter for peak maps.

References VersionInfo::getVersion(), DateTime::now(), and MSExperiment::size().

◆ addLayer() [1/4]

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().

◆ addLayer() [2/4]

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

◆ addLayer() [3/4]

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

◆ addLayer() [4/4]

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

◆ adjustBuffer_()

void adjustBuffer_ ( )

protected

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

◆ changeLayerFilterState

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().

◆ changeLegendVisibility

void changeLegendVisibility ( )

signal

Toggle axis legend visibility change.

◆ changeVisibility

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().

◆ changeVisibleArea_()

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

protectedvirtual

Sets the visible area.

Changes the visible area, adjusts 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.

◆ currentPeakData_()

ExperimentSharedPtrType currentPeakData_ ( )

inlineprotected

Returns the currently active layer (mutable)

◆ dataToWidget_()

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

inlineprotected

Convert chart to widget coordinates.

Translates chart coordinates to widget coordinates.

Parameters

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

References SpectrumCanvas::IM_LOG.

◆ drawText_()

void drawText_	(	QPainter &	painter,
		QStringList	text
	)

protected

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

◆ enterEvent()

void enterEvent ( QEvent * e )

protected

◆ finishAdding_()

virtual bool finishAdding_ ( )

protectedpure virtual

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

Implemented in Spectrum1DCanvas, Spectrum2DCanvas, and Spectrum3DCanvas.

◆ focusOutEvent()

void focusOutEvent ( QFocusEvent * e )

protected

◆ getActionMode()

Int getActionMode ( ) const

inline

Returns the action mode.

Returns the current action mode of type ActionModes

Returns: the current action mode

◆ getCurrentLayer() [1/2]

const LayerData& getCurrentLayer ( ) const

inline

returns the layer data of the active layer

References OPENMS_PRECONDITION.

Referenced by TOPPViewBase::addData(), TOPPViewBase::annotateMS1FromMassFingerprinting_(), TOPPViewBase::annotateWithID(), TOPPViewBase::copyLayer(), TOPPViewBase::editMetadata(), TOPPViewBase::enhancedWorkspaceWindowChanged(), TOPPViewBase::filterContextMenu(), TOPPViewBase::filterEdit(), TOPPViewBase::getCurrentLayer(), TOPPViewBase::layerZoomChanged(), TOPPViewBase::loadFiles(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateToolBar(), and TOPPViewBase::updateViewBar().

◆ getCurrentLayer() [2/2]

LayerData& getCurrentLayer ( )

inline

returns the layer data of the active layer

References OPENMS_PRECONDITION.

◆ getCurrentLayer_()

LayerData& getCurrentLayer_ ( )

inlineprotected

Returns the currently active layer.

◆ getCurrentLayerIndex()

Size getCurrentLayerIndex ( ) const

inline

returns the index of the active layer

Referenced by TOPPViewBase::showCurrentPeaksAs3D().

◆ getCurrentMaxIntensity()

float getCurrentMaxIntensity ( ) const

inline

Returns the maximum intensity of the active layer.

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

◆ getCurrentMinIntensity()

float getCurrentMinIntensity ( ) const

inline

Returns the minimum intensity of the active layer.

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

◆ getDataRange()

const DRange<3>& getDataRange ( )

Returns the area which encloses all data points.

See also: overall_data_range_

◆ getIdentificationMZ_()

double 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)

◆ getIntensityMode()

IntensityModes getIntensityMode ( ) const

inline

Returns the intensity mode.

Returns the current intensity mode of type IntensityModes

Returns: the current intensity mode

Referenced by TOPPViewBase::updateToolBar().

◆ getLayer()

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(), TOPPViewBase::showCurrentPeaksAs3D(), and TOPPViewBase::updateLayerBar().

◆ getLayer_()

LayerData& getLayer_ ( Size index )

inlineprotected

Returns the layer with index index.

References OPENMS_PRECONDITION.

◆ getLayerCount()

Size getLayerCount ( ) const

inline

Returns the number of layers.

Referenced by TOPPViewBase::addData(), IDEvaluationBase::addSearchFile(), TOPPViewBase::enhancedWorkspaceWindowChanged(), TOPPViewBase::fileChanged_(), TOPPViewBase::getFilenamesOfOpenFiles_(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), and TOPPViewBase::updateToolBar().

◆ getLayerFlag() [1/2]

bool getLayerFlag ( LayerData::Flags f ) const

inline

returns a layer flag of the current layer

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

◆ getLayerFlag() [2/2]

bool getLayerFlag	(	Size	layer,
		LayerData::Flags	f
	)		const

inline

returns a layer flag of the layer layer

References OPENMS_PRECONDITION.

◆ getLayerName()

String getLayerName ( Size i )

Gets the name of layer i.

◆ getMaxIntensity()

float 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.

◆ getMinIntensity()

float 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.

◆ getPercentageFactor()

double getPercentageFactor ( )

Returns the percentage factor.

◆ getSnapFactor()

double getSnapFactor ( )

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

See also: snap_factors_

◆ getSpectrumWidget()

SpectrumWidget* getSpectrumWidget ( ) const

inline

Returns the spectrum widget.

Returns the enclosing spectrum widget

Returns: the spectrum widget

◆ getVisibleArea()

const AreaType& getVisibleArea ( ) const

inline

Returns the currently visible area.

See also: visible_area_

Referenced by TOPPViewBase::layerZoomChanged().

◆ getVisibleConsensusData

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_().

◆ getVisibleFeatureData

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_().

◆ getVisibleIdentifications

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.

◆ getVisiblePeakData

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_().

◆ gridLinesShown()

bool gridLinesShown ( ) const

inline

Returns if the grid is currently shown.

Returns: true if the grid is visible, false otherwise

◆ horizontalScrollBarChange

virtual void horizontalScrollBarChange ( int value )

virtualslot

Notifies the canvas that the horizontal scrollbar has been moved.

Reimplement this slot to react on scrollbar events.

◆ intensityModeChange_()

virtual void intensityModeChange_ ( )

protectedvirtual

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

Reimplemented in Spectrum2DCanvas, and Spectrum1DCanvas.

◆ isMzToXAxis()

bool isMzToXAxis ( )

inline

Returns the mapping of m/z to axes.

◆ keyPressEvent()

void keyPressEvent ( QKeyEvent * e )

protected

◆ keyReleaseEvent()

void keyReleaseEvent ( QKeyEvent * e )

protected

◆ layerActivated

void layerActivated ( QWidget * w )

signal

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

◆ layerModficationChange

void layerModficationChange	(	Size	layer,
		bool	modified
	)

signal

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

◆ layerZoomChanged

void layerZoomChanged ( QWidget * w )

signal

Signal emitted whenever the zoom changed.

◆ leaveEvent()

void leaveEvent ( QEvent * e )

protected

◆ modificationStatus_()

void modificationStatus_	(	Size	layer_index,
		bool	modified
	)

protected

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

◆ mzToXAxis()

void mzToXAxis ( bool mz_to_x_axis )

Sets the mapping of m/z to axes.

◆ paintGridLines_()

virtual void paintGridLines_ ( QPainter & painter )

protectedvirtual

Helper function to paint grid lines.

Reimplemented in Spectrum1DCanvas.

◆ preferencesChange

void preferencesChange ( )

signal

Emitted when the layer preferences have changed.

◆ recalculateAxes

void recalculateAxes ( )

signal

Forces recalculation of axis ticks in the connected widget.

◆ recalculateRanges_()

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_

◆ recalculateSnapFactor_()

virtual void recalculateSnapFactor_ ( )

protectedvirtual

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

See also: snap_factors_

Reimplemented in Spectrum2DCanvas, and Spectrum1DCanvas.

◆ removeLayer()

virtual void removeLayer ( Size layer_index )

pure virtual

removes the layer with index layer_index

Referenced by TOPPViewBase::layerContextMenu().

◆ resetZoom

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

◆ resizeEvent()

void resizeEvent ( QResizeEvent * e )

protected

◆ saveCurrentLayer()

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 Spectrum3DCanvas, Spectrum1DCanvas, and Spectrum2DCanvas.

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

◆ sendCursorStatus

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

signal

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

◆ sendStatusMessage

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.

◆ setAdditionalContextMenu

void setAdditionalContextMenu ( QMenu * menu )

slot

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

◆ setCurrentLayerParameters()

void setCurrentLayerParameters ( const Param & param )

inline

Sets the parameters of the current layer.

Referenced by TOPPViewBase::loadFiles().

◆ setFilters()

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().

◆ setIntensityMode()

void setIntensityMode ( IntensityModes mod )

inline

Sets the intensity mode.

Sets the intensity mode

Parameters

mod	the new intensity mode

See also: intensityModeChange_()

◆ setLabel()

void setLabel ( LayerData::LabelType label )

inline

References OPENMS_PRECONDITION.

Referenced by TOPPViewBase::changeLabel().

◆ setLayerFlag() [1/2]

void setLayerFlag	(	LayerData::Flags	f,
		bool	value
	)

inline

sets a layer flag of the current layer

Referenced by TOPPViewBase::changeUnassigned().

◆ setLayerFlag() [2/2]

void setLayerFlag	(	Size	layer,
		LayerData::Flags	f,
		bool	value
	)

inline

sets a layer flag of the layer layer

References OPENMS_PRECONDITION.

◆ setLayerName()

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().

◆ setSpectrumWidget()

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

◆ setVisibleArea

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

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

◆ showCurrentLayerPreferences()

virtual void showCurrentLayerPreferences ( )

pure virtual

Shows the preferences dialog of the active layer.

Implemented in Spectrum3DCanvas, Spectrum1DCanvas, and Spectrum2DCanvas.

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

◆ showGridLines

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().

◆ showMetaData()

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().

◆ translateBackward_()

virtual void translateBackward_ ( )

protectedvirtual

Translation bound to the 'Down' key.

Reimplemented in Spectrum2DCanvas, and Spectrum3DCanvas.

◆ translateForward_()

virtual void translateForward_ ( )

protectedvirtual

Translation bound to the 'Up' key.

Reimplemented in Spectrum2DCanvas, and Spectrum3DCanvas.

◆ translateLeft_()

virtual void translateLeft_ ( Qt::KeyboardModifiers m )

protectedvirtual

Translation bound to the 'Left' key.

Reimplemented in Spectrum2DCanvas, Spectrum1DCanvas, and Spectrum3DCanvas.

◆ translateRight_()

virtual void translateRight_ ( Qt::KeyboardModifiers m )

protectedvirtual

Translation bound to the 'Right' key.

Reimplemented in Spectrum2DCanvas, Spectrum1DCanvas, and Spectrum3DCanvas.

◆ update_()

virtual void update_ ( const char * caller_name )

protectedvirtual

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 in Spectrum3DCanvas.

◆ updateCursor_

void updateCursor_ ( )

protectedslot

Updates the cursor according to the current action mode.

◆ updateHScrollbar

void updateHScrollbar	(	float	,
		float	,
		float	,
		float
	)

signal

Triggers the update of the horizontal scrollbar.

◆ updateLayer

virtual void updateLayer ( Size i )

pure virtualslot

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

Referenced by TOPPViewBase::fileChanged_().

◆ updateScrollbars_()

virtual void updateScrollbars_ ( )

protectedvirtual

Updates the scroll bars.

Updates the scrollbars after a change of the visible area.

Reimplemented in Spectrum1DCanvas, and Spectrum2DCanvas.

◆ updateVScrollbar

void updateVScrollbar	(	float	,
		float	,
		float	,
		float
	)

signal

Triggers the update of the vertical scrollbar.

◆ verticalScrollBarChange

virtual void verticalScrollBarChange ( int value )

virtualslot

Notifies the canvas that the vertical scrollbar has been moved.

Reimplement this slot to react on scrollbar events.

◆ visibleAreaChanged

void visibleAreaChanged ( DRange< 2 > area )

signal

Change of the visible area.

Signal emitted whenever the visible area changes.

Parameters

area	The new visible area.

◆ wheelEvent()

void wheelEvent ( QWheelEvent * e )

protected

◆ widgetToData_() [1/2]

PointType widgetToData_	(	double	x,
		double	y
	)

inlineprotected

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

◆ widgetToData_() [2/2]

PointType widgetToData_ ( const QPoint & pos )

inlineprotected

Calls widgetToData_ with x and y position of pos.

◆ zoom_()

virtual void zoom_	(	int	x,
		int	y,
		bool	zoom_in
	)

protectedvirtual

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

Reimplemented in Spectrum1DCanvas.

◆ zoomAdd_()

void zoomAdd_ ( const AreaType & area )

protected

Add a visible area to the zoom stack.

◆ zoomBack_()

void zoomBack_ ( )

protected

Go backward in zoom history.

◆ zoomClear_()

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.

◆ zoomForward_()

virtual void zoomForward_ ( )

protectedvirtual

Go forward in zoom history.

Reimplemented in Spectrum1DCanvas.

Member Data Documentation

◆ action_mode_

ActionModes action_mode_

protected

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

◆ buffer_

QImage buffer_

protected

Buffer that stores the actual peak information.

◆ context_add_

QMenu* context_add_

protected

External context menu extension.

◆ current_layer_

Size current_layer_

protected

Stores the index of the currently active layer.

◆ intensity_mode_

IntensityModes intensity_mode_

protected

Stores the used intensity mode function.

◆ last_mouse_pos_

QPoint last_mouse_pos_

protected

start position of mouse actions

◆ layers_

std::vector<LayerData> layers_

protected

Layer data.

◆ measurement_start_

PeakIndex measurement_start_

protected

start peak of measuring mode

◆ mz_to_x_axis_

bool mz_to_x_axis_

protected

Stores the mapping of m/z.

◆ overall_data_range_

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).

◆ percentage_factor_

double percentage_factor_

protected

Intensity scaling factor for relative scale with multiple layers.

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

◆ rubber_band_

QRubberBand rubber_band_

protected

Rubber band for selected area.

◆ selected_peak_

PeakIndex selected_peak_

protected

selected peak

◆ show_grid_

bool show_grid_

protected

Stores whether or not to show a grid.

◆ show_timing_

bool show_timing_

protected

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

◆ snap_factors_

std::vector<double> snap_factors_

protected

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

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

◆ spectrum_widget_

SpectrumWidget* spectrum_widget_

protected

Back-pointer to the enclosing spectrum widget.

◆ update_buffer_

bool update_buffer_

protected

Whether to recalculate the data in the buffer when repainting.

◆ visible_area_

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).

◆ zoom_pos_

std::vector<AreaType>::iterator zoom_pos_

protected

The current position in the zoom stack.

◆ zoom_stack_

std::vector<AreaType> zoom_stack_

protected

The zoom stack.

Public Types

Public Slots

Signals

Public Member Functions

Protected Slots

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ AreaType

◆ ConsensusMapSharedPtrType

◆ ConsensusMapType

◆ ExperimentSharedPtrType

◆ ExperimentType

◆ FeatureMapSharedPtrType

◆ FeatureMapType

◆ FeatureType

◆ PeakType

◆ PointType

◆ SpectrumConstIteratorType

◆ SpectrumType

Member Enumeration Documentation

◆ ActionModes

◆ IntensityModes

Constructor & Destructor Documentation

◆ SpectrumCanvas()

◆ ~SpectrumCanvas()

Member Function Documentation

◆ actionModeChange

◆ activateLayer()

◆ activeLayerIndex()

◆ addDataProcessing_()

◆ addLayer() [1/4]

◆ addLayer() [2/4]

◆ addLayer() [3/4]

◆ addLayer() [4/4]

◆ adjustBuffer_()

◆ changeLayerFilterState

◆ changeLegendVisibility

◆ changeVisibility

◆ changeVisibleArea_()

◆ currentPeakData_()

◆ dataToWidget_()

◆ drawText_()

◆ enterEvent()

◆ finishAdding_()

◆ focusOutEvent()

◆ getActionMode()

◆ getCurrentLayer() [1/2]

◆ getCurrentLayer() [2/2]

◆ getCurrentLayer_()

◆ getCurrentLayerIndex()

◆ getCurrentMaxIntensity()

◆ getCurrentMinIntensity()

◆ getDataRange()

◆ getIdentificationMZ_()

◆ getIntensityMode()

◆ getLayer()

◆ getLayer_()

◆ getLayerCount()

◆ getLayerFlag() [1/2]

◆ getLayerFlag() [2/2]

◆ getLayerName()

◆ getMaxIntensity()

◆ getMinIntensity()

◆ getPercentageFactor()

◆ getSnapFactor()

◆ getSpectrumWidget()

◆ getVisibleArea()

◆ getVisibleConsensusData

◆ getVisibleFeatureData

◆ getVisibleIdentifications

◆ getVisiblePeakData

◆ gridLinesShown()

◆ horizontalScrollBarChange

◆ intensityModeChange_()

◆ isMzToXAxis()

◆ keyPressEvent()

◆ keyReleaseEvent()

◆ layerActivated