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

#include <OpenMS/VISUAL/Plot1DCanvas.h>

Inheritance diagram for Plot1DCanvas:

Collaboration diagram for Plot1DCanvas:

Public Types
enum	LabelMode { LM_XABSOLUTE_YABSOLUTE , LM_XPERCENT_YABSOLUTE , LM_XABSOLUTE_YPERCENT , LM_XPERCENT_YPERCENT }
	Label modes (percentage or absolute) of x axis and y axis. More...

enum	DrawModes { DM_PEAKS , DM_CONNECTEDLINES }
	Enumerate all available paint styles. More...

Public Types inherited from PlotCanvas
enum	ActionModes { AM_TRANSLATE , AM_ZOOM , AM_MEASURE }
	Mouse action modes. More...

enum	IntensityModes { IM_NONE , IM_PERCENTAGE , IM_SNAP , IM_LOG }
	Display modes of intensity. More...

typedef LayerData::ExperimentType	ExperimentType
	Main data type (experiment) More...

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

typedef LayerData::ConstExperimentSharedPtrType	ConstExperimentSharedPtrType

typedef LayerData::ODExperimentSharedPtrType	ODExperimentSharedPtrType

typedef LayerData::OSWDataSharedPtrType	OSWDataSharedPtrType

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	activateLayer (Size layer_index) override

void	removeLayer (Size layer_index) override

void	updateLayer (Size i) override

void	setVisibleArea (DRange< 2 > range)
	Sets the visible area. More...

void	horizontalScrollBarChange (int value) override

Public Slots inherited from PlotCanvas
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...

void	dataToWidgetDistance (double x, double y, QPoint &point)
	converts a distance in axis values to pixel values More...

PointType	widgetToDataDistance (double x, double y)
	compute distance in widget coordinates (unit axis as shown) when moving `x/y` px in chart coordinates More...

Signals
void	showCurrentPeaksAs2D ()
	Requests to display all spectra in 2D plot. More...

void	showCurrentPeaksAs3D ()
	Requests to display all spectra in 3D plot. More...

void	showCurrentPeaksAsIonMobility ()
	Requests to display all spectra in ion mobility plot. More...

void	showCurrentPeaksAsDIA ()
	Requests to display all spectra as DIA. More...

Signals inherited from PlotCanvas
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
	Plot1DCanvas (const Param &preferences, QWidget *parent=nullptr)
	Default constructor. More...

	~Plot1DCanvas () override
	Destructor. More...

bool	addChromLayer (ExperimentSharedPtrType chrom_exp_sptr, ODExperimentSharedPtrType ondisc_sptr, OSWDataSharedPtrType chrom_annotation, const int index, const String &filename, const String &caption, const bool multiple_select)

DrawModes	getDrawMode () const
	Returns the draw mode of the current layer. More...

void	setDrawMode (DrawModes mode)
	Sets draw mode of the current layer. More...

void	showCurrentLayerPreferences () override
	Shows the preferences dialog of the active layer. More...

void	saveCurrentLayer (bool visible) override
	Saves the current layer data. More...

bool	flippedLayersExist ()
	Returns whether flipped layers exist or not. More...

void	flipLayer (Size index)
	Flips the layer with `index` up/downwards. More...

bool	mirrorModeActive ()
	Returns whether this widget is currently in mirror mode. More...

void	setMirrorModeActive (bool b)
	Sets whether this widget is currently in mirror mode. More...

void	dataToWidget (const PeakType &peak, QPoint &point, bool flipped=false, bool percentage=true)
	For convenience - calls dataToWidget. More...

void	dataToWidget (double x, double y, QPoint &point, bool flipped=false, bool percentage=false)
	Calls PlotCanvas::dataToWidget_(), takes mirror mode into account. More...

PointType	widgetToData (const QPoint &pos, bool percentage=false)
	For convenience - calls widgetToData. More...

PointType	widgetToData (double x, double y, bool percentage=false)
	Calls PlotCanvas::widgetToData_(), takes mirror mode into account. More...

void	setTextBox (const QString &html)
	Display a static text box on the top right. More...

Annotation1DItem *	addPeakAnnotation (const PeakIndex &peak_index, const QString &text, const QColor &color)
	—– Annotations More...

void	drawAnnotations (Size layer_index, QPainter &painter)
	Draws all annotation items of `layer_index` on `painter`. More...

void	performAlignment (Size layer_index_1, Size layer_index_2, const Param &param)
	—– Alignment More...

void	resetAlignment ()
	Resets alignment_. More...

void	drawAlignment (QPainter &painter)
	Draws the alignment on `painter`. More...

Size	getAlignmentSize ()
	Returns the number of aligned pairs of peaks. More...

double	getAlignmentScore ()
	Returns the score of the alignment. More...

std::vector< std::pair< Size, Size > >	getAlignedPeaksIndices ()
	Returns aligned_peaks_indices_. More...

void	activateSpectrum (Size index, bool repaint=true)
	Sets current spectrum index of current layer to `index`. More...

void	setSwappedAxis (bool swapped)
	is the widget shown vertically? (for projections) More...

void	setCurrentLayerPeakPenStyle (Qt::PenStyle ps)
	Set's the Qt PenStyle of the active layer. More...

void	paint (QPainter paint_device, QPaintEvent e)
	Actual painting takes place here. More...

void	setDrawInterestingMZs (bool enable)
	interesting (e.g., high-intensity) get live annotated with m/s's More...

bool	isDrawInterestingMZs () const
	Return true if interesting m/s are annotated. More...

void	setIonLadderVisible (bool show)

bool	isIonLadderVisible () const

Public Member Functions inherited from PlotCanvas
	PlotCanvas (const Param &preferences, QWidget *parent=nullptr)
	Default constructor. More...

	~PlotCanvas () override
	Destructor. More...

void	setPlotWidget (PlotWidget *widget)
	Sets the spectrum widget. More...

PlotWidget *	getPlotWidget () 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...

LayerData &	getLayer (Size index)
	returns the layer data with index `index` More...

const LayerData &	getCurrentLayer () const
	returns the layer data of the active layer More...

LayerData &	getCurrentLayer ()
	returns the layer data of the active layer More...

Size	getCurrentLayerIndex () const
	returns the index of the active layer More...

bool	getLayerFlag (LayerData::Flags f) const
	returns a layer flag of the current layer More...

void	setLayerFlag (LayerData::Flags f, bool value)
	sets a layer flag of the current layer More...

bool	getLayerFlag (Size layer, LayerData::Flags f) const
	returns a layer flag of the layer `layer` More...

void	setLayerFlag (Size layer, LayerData::Flags f, bool value)
	sets a layer flag of the layer `layer` More...

void	setLabel (LayerData::LabelType label)

const AreaType &	getVisibleArea () const
	Returns the currently visible area. More...

virtual void	setFilters (const DataFilters &filters)
	Sets the filters applied to the data before drawing (for the current layer) More...

bool	isMzToXAxis ()
	Returns the mapping of m/z to axes. More...

void	mzToXAxis (bool mz_to_x_axis)
	Sets the mapping of m/z to axes. More...

Size	getLayerCount () const
	Returns the number of layers. More...

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...

void	removeLayers ()
	removes all layers by calling removeLayer() for all layer indices (from highest to lowest) More...

bool	addLayer (ExperimentSharedPtrType map, ODExperimentSharedPtrType od_map, const String &filename="")
	Add a peak data layer. More...

bool	addLayer (FeatureMapSharedPtrType map, const String &filename="")
	Add a feature data layer. More...

bool	addLayer (ConsensusMapSharedPtrType map, const String &filename="")
	Add a consensus feature data layer. More...

bool	addLayer (std::vector< PeptideIdentification > &peptides, const String &filename="")
	Add an identification data layer. More...

float	getCurrentMinIntensity () const
	Returns the minimum intensity of the active layer. More...

float	getCurrentMaxIntensity () const
	Returns the maximum intensity of the active layer. More...

float	getMinIntensity (Size index) const
	Returns the minimum intensity of the layer with index `index`. More...

float	getMaxIntensity (Size index) const
	Returns the maximum intensity of the layer with index `index`. More...

void	setLayerName (Size i, const String &name)
	Sets the `name` of layer `i`. More...

String	getLayerName (Size i)
	Gets the name of layer `i`. More...

void	setCurrentLayerParameters (const Param &param)
	Sets the parameters of the current layer. More...

const DRange< 3 > &	getDataRange ()
	Returns the area which encloses all data points. More...

double	getSnapFactor ()
	Returns the first intensity scaling factor for 'snap to maximum intensity mode'. More...

double	getPercentageFactor ()
	Returns the percentage factor. More...

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

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

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

virtual	~DefaultParamHandler ()
	Destructor. More...

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

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

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

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

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

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

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

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

Static Public Attributes
constexpr static double	TOP_MARGIN {1.09}
	extra empty margin added on top to ensure annotations and 100% y-axis label are properly drawn More...

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

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

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

void	drawCoordinates_ (QPainter &painter, const PeakIndex &peak)
	Draws the coordinates (or coordinate deltas) to the widget's upper left corner. More...

void	drawDeltas_ (QPainter &painter, const PeakIndex &start, const PeakIndex &end)
	Draws the coordinates (or coordinate deltas) to the widget's upper left corner. More...

void	drawMZAtInterestingPeaks_ (Size layer_index, QPainter &painter)
	annotate interesting peaks in visible area with m/z More...

void	changeVisibleArea_ (double lo, double hi, bool repaint=true, bool add_to_stack=false)
	Changes visible area interval. More...

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) More...

void	drawDashedLine_ (const QPoint &from, const QPoint &to, QPainter &painter)
	Draws a dashed line using the highlighted peak color parameter. More...

void	updatePercentageFactor_ (Size layer_index)
	Recalculates the current scale factor based on the specified layer (= 1.0 if intensity mode != IM_PERCENTAGE) More...

void	changeVisibleArea_ (const AreaType &new_area, bool repaint=true, bool add_to_stack=false) override
	Sets the visible area. More...

void	recalculateSnapFactor_ () override
	Recalculates the intensity scaling factor for 'snap to maximum intensity mode'. More...

void	updateScrollbars_ () override
	Updates the scroll bars. More...

void	intensityModeChange_ () override
	This method is called whenever the intensity mode changes. Reimplement if you need to react on such changes. More...

PeakIndex	findPeakAtPosition_ (QPoint)
	Find peak next to the given position. More...

void	addUserLabelAnnotation_ (const QPoint &screen_position)
	Shows dialog and calls addLabelAnnotation_. More...

void	addLabelAnnotation_ (const QPoint &screen_position, QString label_text)
	Adds an annotation item at the given screen position. More...

void	addUserPeakAnnotation_ (PeakIndex near_peak)
	Shows dialog and calls addPeakAnnotation_. More...

void	ensureAnnotationsWithinDataRange_ ()
	Ensure that all annotations are within data range. More...

Reimplemented QT events
void	paintEvent (QPaintEvent *e) override

void	mousePressEvent (QMouseEvent *e) override

void	mouseReleaseEvent (QMouseEvent *e) override

void	mouseMoveEvent (QMouseEvent *e) override

void	keyPressEvent (QKeyEvent *e) override

void	contextMenuEvent (QContextMenuEvent *e) override

void	zoomForward_ () override
	Go forward in zoom history. More...

void	zoom_ (int x, int y, bool zoom_in) override
	docu in base class More...

void	translateLeft_ (Qt::KeyboardModifiers m) override
	Translation bound to the 'Left' key. More...

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

void	paintGridLines_ (QPainter &painter) override
	Helper function to paint grid lines. More...

Protected Member Functions inherited from PlotCanvas
void	resizeEvent (QResizeEvent *e) override

void	wheelEvent (QWheelEvent *e) override

void	keyPressEvent (QKeyEvent *e) override

void	keyReleaseEvent (QKeyEvent *e) override

void	focusOutEvent (QFocusEvent *e) override

void	leaveEvent (QEvent *e) override

void	enterEvent (QEvent *e) override

void	zoomBack_ ()
	Go backward in zoom history. More...

void	zoomAdd_ (const AreaType &area)
	Add a visible area to the zoom stack. More...

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

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

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

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

void	drawText_ (QPainter &painter, QStringList text)
	Draws several lines of text to the upper right corner of the widget. More...

double	getIdentificationMZ_ (const Size layer_index, const PeptideIdentification &peptide) const
	Returns the m/z value of an identification depending on the m/z source of the layer (precursor mass/theoretical peptide mass) More...

void	popIncompleteLayer_ (const QString &error_message="")

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
std::vector< DrawModes >	draw_modes_
	Draw modes (for each layer) More...

std::vector< Qt::PenStyle >	peak_penstyle_
	Draw style (for each layer) More...

QPoint	measurement_start_point_
	start point of "ruler" for measure mode More...

bool	mirror_mode_
	Indicates whether this widget is currently in mirror mode. More...

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

bool	show_alignment_
	Indicates whether an alignment is currently visualized. More...

Size	alignment_layer_1_
	Layer index of the first alignment layer. More...

Size	alignment_layer_2_
	Layer index of the second alignment layer. More...

std::vector< std::pair< double, double > >	aligned_peaks_mz_delta_
	Stores the alignment as MZ values of pairs of aligned peaks in both spectra. More...

std::vector< std::pair< Size, Size > >	aligned_peaks_indices_
	Stores the peak indices of pairs of aligned peaks in both spectra. More...

double	alignment_score_
	Stores the score of the last alignment. More...

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

bool	ion_ladder_visible_
	whether the ion ladder is displayed on the top right corner in ID view More...

bool	draw_interesting_MZs_
	annotate interesting peaks with m/z's More...

QTextDocument	text_box_content_

Protected Attributes inherited from PlotCanvas
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...

LayerStack	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...

PlotWidget *	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...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
	Writes all parameters to meta values. More...

Detailed Description

Canvas for visualization of one or several spectra.

The example image shows Plot1DCanvas 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

◆ DrawModes

enum DrawModes

Enumerate all available paint styles.

Enumerator
DM_PEAKS	draw data as peak
DM_CONNECTEDLINES	draw as connected lines

◆ LabelMode

enum LabelMode

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

Enumerator
LM_XABSOLUTE_YABSOLUTE
LM_XPERCENT_YABSOLUTE
LM_XABSOLUTE_YPERCENT
LM_XPERCENT_YPERCENT

Constructor & Destructor Documentation

◆ Plot1DCanvas()

Plot1DCanvas	(	const Param &	preferences,
		QWidget *	parent = `nullptr`
	)

Default constructor.

◆ ~Plot1DCanvas()

~Plot1DCanvas ( )

override

Destructor.

Member Function Documentation

◆ activateLayer

void activateLayer ( Size layer_index )

overrideslot

◆ activateSpectrum()

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

Sets current spectrum index of current layer to index.

Referenced by TOPPViewBase::addData().

◆ addChromLayer()

bool addChromLayer	(	ExperimentSharedPtrType	chrom_exp_sptr,
		ODExperimentSharedPtrType	ondisc_sptr,
		OSWDataSharedPtrType	chrom_annotation,
		const int	index,
		const String &	filename,
		const String &	caption,
		const bool	multiple_select
	)

add a chromatogram layer

Parameters

chrom_exp_sptr	An MSExperiment with chromatograms
ondisc_sptr	OnDisk experiment, as fallback to read the chromatogram from, should `chrom_exp_sptr.getChromatograms(index)` be empty
OSWDataSharedPtrType	If OSWData was loaded, pass the shared_pointer from the LayerData. Otherwise leave empty.
index	Index of the chromatogram to show
filename	For file change watcher (can be empty, if need be)
caption	Name of layer
multiple_select	.... not sure ...

Returns: true on success, false if data was missing etc

Note: : this does NOT trigger layerActivated signal for efficiency-reasons. Do it manually afterwards!

◆ addLabelAnnotation_()

void addLabelAnnotation_	(	const QPoint &	screen_position,
		QString	label_text
	)

protected

Adds an annotation item at the given screen position.

◆ addPeakAnnotation()

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

—– Annotations

Add an annotation item for the given peak

◆ addUserLabelAnnotation_()

void addUserLabelAnnotation_ ( const QPoint & screen_position )

protected

Shows dialog and calls addLabelAnnotation_.

◆ addUserPeakAnnotation_()

void addUserPeakAnnotation_ ( PeakIndex near_peak )

protected

Shows dialog and calls addPeakAnnotation_.

◆ changeVisibleArea_() [1/2]

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

overrideprotectedvirtual

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 repainting of the widget should be triggered
add_to_stack	If the new area is to add to the zoom_stack_

Reimplemented from PlotCanvas.

◆ changeVisibleArea_() [2/2]

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) .

◆ contextMenuEvent()

void contextMenuEvent ( QContextMenuEvent * e )

overrideprotected

◆ currentLayerParamtersChanged_

void currentLayerParamtersChanged_ ( )

protectedslot

Reacts on changed layer parameters.

◆ dataToWidget() [1/2]

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

For convenience - calls dataToWidget.

◆ dataToWidget() [2/2]

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

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

◆ drawAlignment()

void drawAlignment ( QPainter & painter )

Draws the alignment on painter.

◆ drawAnnotations()

void drawAnnotations	(	Size	layer_index,
		QPainter &	painter
	)

Draws all annotation items of layer_index on painter.

◆ drawCoordinates_()

void drawCoordinates_	(	QPainter &	painter,
		const PeakIndex &	peak
	)

protected

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

◆ drawDashedLine_()

void drawDashedLine_	(	const QPoint &	from,
		const QPoint &	to,
		QPainter &	painter
	)

protected

Draws a dashed line using the highlighted peak color parameter.

◆ drawDeltas_()

void drawDeltas_	(	QPainter &	painter,
		const PeakIndex &	start,
		const PeakIndex &	end
	)

protected

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

◆ drawHighlightedPeak_()

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)

◆ drawMZAtInterestingPeaks_()

void drawMZAtInterestingPeaks_	(	Size	layer_index,
		QPainter &	painter
	)

protected

annotate interesting peaks in visible area with m/z

◆ ensureAnnotationsWithinDataRange_()

void ensureAnnotationsWithinDataRange_ ( )

protected

Ensure that all annotations are within data range.

◆ findPeakAtPosition_()

PeakIndex findPeakAtPosition_ ( QPoint )

protected

Find peak next to the given position.

◆ finishAdding_()

bool finishAdding_ ( )

overrideprotectedvirtual

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

Implements PlotCanvas.

◆ flipLayer()

void flipLayer ( Size index )

Flips the layer with index up/downwards.

◆ flippedLayersExist()

bool flippedLayersExist ( )

Returns whether flipped layers exist or not.

◆ getAlignedPeaksIndices()

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

Returns aligned_peaks_indices_.

◆ getAlignmentScore()

double getAlignmentScore ( )

Returns the score of the alignment.

Referenced by TOPPViewBase::showSpectrumAlignmentDialog().

◆ getAlignmentSize()

Size getAlignmentSize ( )

Returns the number of aligned pairs of peaks.

Referenced by TOPPViewBase::showSpectrumAlignmentDialog().

◆ getDrawMode()

DrawModes getDrawMode ( ) const

Returns the draw mode of the current layer.

Referenced by TOPPViewBase::updateToolBar().

◆ horizontalScrollBarChange

void horizontalScrollBarChange ( int value )

overrideslot

◆ intensityModeChange_()

void intensityModeChange_ ( )

overrideprotectedvirtual

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

Reimplemented from PlotCanvas.

◆ isDrawInterestingMZs()

bool isDrawInterestingMZs ( ) const

Return true if interesting m/s are annotated.

◆ isIonLadderVisible()

bool isIonLadderVisible ( ) const

◆ keyPressEvent()

void keyPressEvent ( QKeyEvent * e )

overrideprotected

◆ mirrorModeActive()

bool mirrorModeActive ( )

Returns whether this widget is currently in mirror mode.

Referenced by TOPPViewBase::showSpectrumAlignmentDialog().

◆ mouseMoveEvent()

void mouseMoveEvent ( QMouseEvent * e )

overrideprotected

◆ mousePressEvent()

void mousePressEvent ( QMouseEvent * e )

overrideprotected

◆ mouseReleaseEvent()

void mouseReleaseEvent ( QMouseEvent * e )

overrideprotected

◆ paint()

void paint	(	QPainter *	paint_device,
		QPaintEvent *	e
	)

Actual painting takes place here.

◆ paintEvent()

void paintEvent ( QPaintEvent * e )

overrideprotected

◆ paintGridLines_()

void paintGridLines_ ( QPainter & painter )

overrideprotectedvirtual

Helper function to paint grid lines.

Reimplemented from PlotCanvas.

◆ performAlignment()

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

◆ recalculateSnapFactor_()

void recalculateSnapFactor_ ( )

overrideprotectedvirtual

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

See also: snap_factors_

Reimplemented from PlotCanvas.

◆ removeLayer

void removeLayer ( Size layer_index )

overrideslot

◆ resetAlignment()

void resetAlignment ( )

Resets alignment_.

◆ saveCurrentLayer()

void saveCurrentLayer ( bool visible )

overridevirtual

Saves the current layer data.

Parameters

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

Implements PlotCanvas.

◆ setCurrentLayerPeakPenStyle()

void setCurrentLayerPeakPenStyle ( Qt::PenStyle ps )

Set's the Qt PenStyle of the active layer.

◆ setDrawInterestingMZs()

void setDrawInterestingMZs ( bool enable )

interesting (e.g., high-intensity) get live annotated with m/s's

◆ setDrawMode()

void setDrawMode ( DrawModes mode )

Sets draw mode of the current layer.

Referenced by TOPPViewBase::setDrawMode1D().

◆ setIonLadderVisible()

void setIonLadderVisible ( bool show )

◆ setMirrorModeActive()

void setMirrorModeActive ( bool b )

Sets whether this widget is currently in mirror mode.

◆ setSwappedAxis()

void setSwappedAxis ( bool swapped )

is the widget shown vertically? (for projections)

◆ setTextBox()

void setTextBox ( const QString & html )

Display a static text box on the top right.

◆ setVisibleArea

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

◆ showCurrentLayerPreferences()

void showCurrentLayerPreferences ( )

overridevirtual

Shows the preferences dialog of the active layer.

Implements PlotCanvas.

◆ showCurrentPeaksAs2D

void showCurrentPeaksAs2D ( )

signal

Requests to display all spectra in 2D plot.

◆ showCurrentPeaksAs3D

void showCurrentPeaksAs3D ( )

signal

Requests to display all spectra in 3D plot.

◆ showCurrentPeaksAsDIA

void showCurrentPeaksAsDIA ( )

signal

Requests to display all spectra as DIA.

◆ showCurrentPeaksAsIonMobility

void showCurrentPeaksAsIonMobility ( )

signal

Requests to display all spectra in ion mobility plot.

◆ translateLeft_()

void translateLeft_ ( Qt::KeyboardModifiers m )

overrideprotectedvirtual

Translation bound to the 'Left' key.

Reimplemented from PlotCanvas.

◆ translateRight_()

void translateRight_ ( Qt::KeyboardModifiers m )

overrideprotectedvirtual

Translation bound to the 'Right' key.

Reimplemented from PlotCanvas.

◆ updateLayer

void updateLayer ( Size i )

overrideslot

◆ updatePercentageFactor_()

void updatePercentageFactor_ ( Size layer_index )

protected

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

◆ updateScrollbars_()

void updateScrollbars_ ( )

overrideprotectedvirtual

Updates the scroll bars.

Updates the scrollbars after a change of the visible area.

Reimplemented from PlotCanvas.

◆ widgetToData() [1/2]

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

For convenience - calls widgetToData.

◆ widgetToData() [2/2]

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

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

◆ zoom_()

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

overrideprotectedvirtual

docu in base class

Reimplemented from PlotCanvas.

◆ zoomForward_()

void zoomForward_ ( )

overrideprotectedvirtual

Go forward in zoom history.

Reimplemented from PlotCanvas.

Member Data Documentation

◆ aligned_peaks_indices_

std::vector<std::pair<Size, Size> > aligned_peaks_indices_

protected

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

◆ aligned_peaks_mz_delta_

std::vector<std::pair<double, double> > aligned_peaks_mz_delta_

protected

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

◆ alignment_layer_1_

Size alignment_layer_1_

protected

Layer index of the first alignment layer.

◆ alignment_layer_2_

Size alignment_layer_2_

protected

Layer index of the second alignment layer.

◆ alignment_score_

double alignment_score_

protected

Stores the score of the last alignment.

◆ draw_interesting_MZs_

bool draw_interesting_MZs_

protected

annotate interesting peaks with m/z's

◆ draw_modes_

std::vector<DrawModes> draw_modes_

protected

Draw modes (for each layer)

◆ ion_ladder_visible_

bool ion_ladder_visible_

protected

whether the ion ladder is displayed on the top right corner in ID view

◆ is_swapped_

bool is_swapped_

protected

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

◆ measurement_start_point_

QPoint measurement_start_point_

protected

start point of "ruler" for measure mode

◆ mirror_mode_

bool mirror_mode_

protected

Indicates whether this widget is currently in mirror mode.

◆ moving_annotations_

bool moving_annotations_

protected

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

◆ peak_penstyle_

std::vector<Qt::PenStyle> peak_penstyle_

protected

Draw style (for each layer)

◆ show_alignment_

bool show_alignment_

protected

Indicates whether an alignment is currently visualized.

◆ text_box_content_

QTextDocument text_box_content_

protected

◆ TOP_MARGIN

constexpr static double TOP_MARGIN {1.09}

staticconstexpr

extra empty margin added on top to ensure annotations and 100% y-axis label are properly drawn

Public Types

Public Slots

Signals

Public Member Functions

Static Public Attributes

Protected Slots

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ DrawModes

◆ LabelMode

Constructor & Destructor Documentation

◆ Plot1DCanvas()

◆ ~Plot1DCanvas()

Member Function Documentation

◆ activateLayer

◆ activateSpectrum()

◆ addChromLayer()

◆ addLabelAnnotation_()

◆ addPeakAnnotation()

◆ addUserLabelAnnotation_()

◆ addUserPeakAnnotation_()

◆ changeVisibleArea_() [1/2]

◆ changeVisibleArea_() [2/2]

◆ contextMenuEvent()

◆ currentLayerParamtersChanged_

◆ dataToWidget() [1/2]

◆ dataToWidget() [2/2]

◆ drawAlignment()

◆ drawAnnotations()

◆ drawCoordinates_()

◆ drawDashedLine_()

◆ drawDeltas_()

◆ drawHighlightedPeak_()

◆ drawMZAtInterestingPeaks_()

◆ ensureAnnotationsWithinDataRange_()

◆ findPeakAtPosition_()

◆ finishAdding_()

◆ flipLayer()

◆ flippedLayersExist()

◆ getAlignedPeaksIndices()

◆ getAlignmentScore()

◆ getAlignmentSize()

◆ getDrawMode()

◆ horizontalScrollBarChange

◆ intensityModeChange_()

◆ isDrawInterestingMZs()

◆ isIonLadderVisible()

◆ keyPressEvent()

◆ mirrorModeActive()

◆ mouseMoveEvent()

◆ mousePressEvent()

◆ mouseReleaseEvent()

◆ paint()

◆ paintEvent()

◆ paintGridLines_()

◆ performAlignment()

◆ recalculateSnapFactor_()

◆ removeLayer

◆ resetAlignment()

◆ saveCurrentLayer()

◆ setCurrentLayerPeakPenStyle()

◆ setDrawInterestingMZs()

◆ setDrawMode()

◆ setIonLadderVisible()

◆ setMirrorModeActive()

◆ setSwappedAxis()

◆ setTextBox()

◆ setVisibleArea

◆ showCurrentLayerPreferences()

◆ showCurrentPeaksAs2D

◆ showCurrentPeaksAs3D

◆ showCurrentPeaksAsDIA

◆ showCurrentPeaksAsIonMobility

◆ translateLeft_()

◆ translateRight_()

◆ updateLayer

◆ updatePercentageFactor_()