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 LayerDataBase::ExperimentType	ExperimentType
	Main data type (experiment) More...

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

typedef LayerDataBase::ConstExperimentSharedPtrType	ConstExperimentSharedPtrType

typedef LayerDataBase::ODExperimentSharedPtrType	ODExperimentSharedPtrType

typedef LayerDataBase::FeatureMapType	FeatureMapType
	Main data type (features) More...

typedef LayerDataBase::FeatureMapSharedPtrType	FeatureMapSharedPtrType
	Main managed data type (features) More...

typedef LayerDataBase::ConsensusMapType	ConsensusMapType
	Main data type (consensus features) More...

typedef LayerDataBase::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...

using	RangeType = RangeAllType
	a generic range for the most common units More...

using	AreaXYType = Area< 2 >::AreaXYType
	The range of data shown on the X and Y axis (unit depends on runtime config) More...

using	VisibleArea = Area< 2 >
	The visible range of data on X and Y axis as shown on plot axis (not necessarily the range of actual data, e.g. no data to show). More...

using	GenericArea = Area< 2 >
	A generic range of data on X and Y axis as shown on plot axis. More...

using	PixelArea = Area< 2 >

using	UnitRange = RangeAllType

using	PointOnAxis = DimMapper< 2 >::Point

Public Slots
void	activateLayer (Size layer_index) override

void	removeLayer (Size layer_index) override

void	updateLayer (Size i) override

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	setVisibleArea (const VisibleArea &area)
	Sets the visible area. More...

void	setVisibleArea (const RangeAllType &area)
	Sets the visible area. More...

void	setVisibleArea (const AreaXYType &area)
	Sets the visible area. More...

void	setVisibleAreaX (double min, double max)
	Set only the visible area for the x axis; other axes are untouched. More...

void	setVisibleAreaY (double min, double max)
	Set only the visible area for the y axis; other axes are untouched. More...

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

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

AreaXYType	canvasPixelArea () const
	Get the Area in pixel coordinates of the current canvas for X and Y axis. More...

const DimMapper< 2 > &	getMapper () const
	Get Mapper to translate between values for axis (X/Y) and units (m/z, RT, intensity, ...) More...

void	setMapper (const DimMapper< 2 > &mapper)
	Set a new mapper for the canvas. 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 (const MSSpectrum &spec)
	Requests to display this spectrum (=frame) in ion mobility plot. More...

void	showCurrentPeaksAsDIA (const Precursor &pc, const MSExperiment &exp)
	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 (const VisibleArea &area)
	Change of the visible area. More...

void	sendCursorStatus (const String &x_value, const String &y_value)
	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 f_min, float disp_min, float disp_max, float f_max)
	Triggers the update of the vertical scrollbar. More...

void	updateHScrollbar (float f_min, float disp_min, float disp_max, float f_max)
	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, const DIM gravity_axis=DIM::Y, QWidget *parent=nullptr)
	Default constructor. More...

	~Plot1DCanvas () override
	Destructor. More...

const LayerData1DBase &	getLayer (Size index) const

LayerData1DBase &	getLayer (Size index)

const LayerData1DBase &	getCurrentLayer () const

LayerData1DBase &	getCurrentLayer ()

const DimBase &	getGravityDim () const
	Get the dimension on which gravity is currently acting upon (usually it's the Y axis' unit) More...

const DimBase &	getNonGravityDim () const
	Get the dimension on which gravity is currently not acting upon (the orthogonal axis; usually it's the X axis' unit) More...

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

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...

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

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

bool	mirrorModeActive () const
	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 DPosition< 2 > &peak, QPoint &point, bool flipped=false)
	For convenience - calls dataToWidget. More...

void	dataToWidget (const DPosition< 2 > &xy_point, DPosition< 2 > &point, bool flipped)
	For convenience - calls dataToWidget. More...

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

PointXYType	widgetToData (const QPoint &pos)
	For convenience - calls widgetToData. More...

PointXYType	widgetToData (double x, double y)
	Calls PlotCanvas::widgetToData_(), takes mirror mode into account. More...

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

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

template<class T >
void	pushIntoDataRange (T &data_point, const int layer_index)
	Pushes a data point back into the valid data range of the current layer area. Useful for annotation items which were mouse-dragged outside the range by the user. More...

void	pushIntoDataRange (PointXYType &xy_unit, const int layer_index)
	Pushes a data point back into the valid data range of the current layer area. Useful for annotation items which were mouse-dragged outside the range by the user. 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	performAlignment (Size layer_index_1, Size layer_index_2, const Param &param)

void	resetAlignment ()
	Resets alignment_. More...

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

double	getAlignmentScore () const
	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	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

const Gravitator &	getGravitator () const
	Get gravity manipulation object to apply gravity to points. More...

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

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

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

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

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

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

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

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

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

void	setLabel (LayerDataBase::LabelType label)

const VisibleArea &	getVisibleArea () const
	Returns the currently visible area. This is the authority which determines the X and Y axis' scale. More...

bool	isVisible (const PointOnAxis &p) const

PixelArea	getPixelRange () const

virtual void	setFilters (const DataFilters &filters)
	Sets the filters applied to the data before drawing (for the current layer) 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 (std::unique_ptr< LayerData1DBase > layer)
	Add an already constructed layer (e.g. for projections) More...

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

bool	addChromLayer (const ExperimentSharedPtrType &map, ODExperimentSharedPtrType od_map, const String &filename="")
	Add a chrom 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 RangeType &	getDataRange () const
	Returns the area which encloses all data points of all layers. More...

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

double	getPercentageFactor () const
	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...

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
void	dataToWidget_ (double x, double y, QPoint &point)
	Convert chart to widget coordinates. More...

void	dataToWidget_ (const DPosition< 2 > &xy, QPoint &point)

QPoint	dataToWidget_ (const DPosition< 2 > &xy)

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

void	changeVisibleAreaCommon_ (const UnitRange &new_area, bool repaint, bool add_to_stack)
	internal method, called before calling parent function PlotCanvas::changeVisibleArea_ More...

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

void	changeVisibleArea_ (const AreaXYType &new_area, bool repaint=true, bool add_to_stack=false)
	Changes visible area interval. More...

void	changeVisibleArea_ (const UnitRange &new_area, 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	resetZoom (bool repaint=true) override
	Zooms fully out and resets the zoom stack. More...

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

void	recalculateRanges_ () override
	Recalculates the overall_data_range_ (by calling PlotCanvas::recalculateRanges_) plus the overall_data_range_1d_ (which only takes into account the current spec/chrom/.. of all layers) 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...

RangeAllType	correctGravityAxisOfVisibleArea_ (UnitRange area)

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	dimensionsChanged_ ()
	Call this whenever the DimMapper receives new dimensions; will update the axes and scrollbars. More...

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

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

void	zoomAdd_ (const VisibleArea &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...

PointXYType	widgetToData_ (double x, double y)
	Convert widget (pixel) to chart (unit) coordinates. More...

PointXYType	widgetToData_ (const QPoint &pos)
	Calls widgetToData_ with x and y position of `pos`. 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, const 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...

Reimplemented QT events
class	Painter1DChrom

class	Painter1DPeak

class	Painter1DIonMobility

RangeType	overall_data_range_1d_
	The data range (m/z, RT and intensity) of the current(!) spec/chrom for all layers. More...

std::vector< DrawModes >	draw_modes_
	Draw modes (for each layer) - sticks or connected lines. More...

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

QPoint	measurement_start_point_px_
	start point of "ruler" in pixel coordinates for measure mode More...

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

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

bool	show_alignment_ = false
	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_ = 0.0
	Stores the score of the last alignment. More...

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

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

QTextDocument	text_box_content_
	The text box in the upper left corner with the current data coordinates of the cursor. More...

Gravitator	gr_
	handles pulling/pushing of points to the edges of the widget More...

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
	Zooms such that screen point x, y would still point to the same data point. 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	translateForward_ () override
	Translation bound to the 'Up' key. More...

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

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

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

Protected Attributes inherited from PlotCanvas
QImage	buffer_
	Buffer that stores the actual peak information. More...

DimMapper< 2 >	unit_mapper_
	Mapper for X and Y axis. More...

ActionModes	action_mode_ = AM_TRANSLATE
	Stores the current action mode (Pick, Zoom, Translate) More...

IntensityModes	intensity_mode_ = IM_NONE
	Stores the used intensity mode function. More...

LayerStack	layers_
	Layer data. More...

VisibleArea	visible_area_
	Stores the currently visible area in data units (e.g. seconds, m/z, intensity etc) and axis (X,Y) area. More...

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

bool	show_grid_ = true
	Stores whether or not to show a grid. More...

std::vector< VisibleArea >	zoom_stack_
	The zoom stack. More...

std::vector< VisibleArea >::iterator	zoom_pos_ = zoom_stack_.end()
	The current position in the zoom stack. More...

bool	update_buffer_ = false
	Whether to recalculate the data in the buffer when repainting. More...

PlotWidget *	spectrum_widget_ = nullptr
	Back-pointer to the enclosing spectrum widget. More...

QPoint	last_mouse_pos_
	start position of mouse actions More...

double	percentage_factor_ = 1.0
	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_ = nullptr
	External context menu extension. More...

bool	show_timing_ = false
	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

Canvas for visualization of one or several spectra.

The example image shows Plot1DCanvas displaying a raw data layer and a peak data layer.

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.

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,
		const DIM	gravity_axis = `DIM::Y`,
		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 &	basename,
		const String &	basename_extra
	)

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
chrom_annotation	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)
basename	Name of layer (usually the basename of the file)
basename_extra	Optional suffix of the layer name (e.g. a peptide sequence, or an index '[39]).

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,
		const 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_() [1/3]

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

protected

Changes visible area interval.

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

◆ changeVisibleArea_() [2/3]

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

protected

Changes visible area interval.

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

◆ changeVisibleArea_() [3/3]

void changeVisibleArea_	(	VisibleArea	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 the area is outside the overall data range, the new area is pushed back into the overall range.

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 from PlotCanvas.

◆ changeVisibleAreaCommon_()

void changeVisibleAreaCommon_	(	const UnitRange &	new_area,
		bool	repaint,
		bool	add_to_stack
	)

protected

internal method, called before calling parent function PlotCanvas::changeVisibleArea_

◆ contextMenuEvent()

void contextMenuEvent ( QContextMenuEvent * e )

overrideprotected

◆ correctGravityAxisOfVisibleArea_()

RangeAllType correctGravityAxisOfVisibleArea_ ( UnitRange area )

protected

Adjust the gravity axis (usually y-axis with intensity) according to the given range on the x-axis (since the user cannot freely choose the limits of this axis in 1D View)

◆ currentLayerParamtersChanged_

void currentLayerParamtersChanged_ ( )

protectedslot

Reacts on changed layer parameters.

◆ dataToWidget() [1/3]

void dataToWidget	(	const DPosition< 2 > &	peak,
		QPoint &	point,
		bool	flipped = `false`
	)

For convenience - calls dataToWidget.

Referenced by Annotation1DCaret< DataPoint >::draw(), and Annotation1DPeakItem< DataPoint >::draw().

◆ dataToWidget() [2/3]

void dataToWidget	(	const DPosition< 2 > &	xy_point,
		DPosition< 2 > &	point,
		bool	flipped
	)

For convenience - calls dataToWidget.

◆ dataToWidget() [3/3]

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

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

◆ dataToWidget_() [1/3]

QPoint dataToWidget_ ( const DPosition< 2 > & xy )

inlineprotected

References DPosition< D, TCoordinateType >::getX(), and DPosition< D, TCoordinateType >::getY().

◆ dataToWidget_() [2/3]

void dataToWidget_	(	const DPosition< 2 > &	xy,
		QPoint &	point
	)

inlineprotected

References DPosition< D, TCoordinateType >::getX(), and DPosition< D, TCoordinateType >::getY().

◆ dataToWidget_() [3/3]

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

inlineprotected

Convert chart to widget coordinates.

Translates chart (unit) coordinates to widget (pixel) coordinates.

Parameters

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

References PlotCanvas::IM_LOG.

◆ dataToWidgetDistance()

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

inline

converts a distance in axis values to pixel values

◆ drawAlignment_()

void drawAlignment_ ( QPainter & painter )

protected

Draws the alignment on painter.

◆ drawCoordinates_()

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

protected

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

◆ 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)

◆ 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 ( ) const

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().

◆ getCurrentLayer() [1/2]

LayerData1DBase& getCurrentLayer ( )

returns the layer data of the active layer

Exceptions

std::bad_cast exception if the current layer is not a LayerData1DBase

◆ getCurrentLayer() [2/2]

const LayerData1DBase& getCurrentLayer ( ) const

returns the layer data of the active layer

Exceptions

std::bad_cast exception if the current layer is not a LayerData1DBase

◆ getDrawMode()

DrawModes getDrawMode ( ) const

Returns the draw mode of the current layer.

Referenced by TOPPViewBase::updateToolBar().

◆ getGravitator()

const Gravitator& getGravitator ( ) const

inline

Get gravity manipulation object to apply gravity to points.

Returns: Gravitator

Referenced by Annotation1DPeakItem< DataPoint >::draw().

◆ getGravityDim()

const DimBase& getGravityDim ( ) const

Get the dimension on which gravity is currently acting upon (usually it's the Y axis' unit)

◆ getLayer() [1/2]

LayerData1DBase& getLayer ( Size index )

returns the layer data of the layer index

Exceptions

std::bad_cast exception if the current layer is not a LayerData1DBase

◆ getLayer() [2/2]

const LayerData1DBase& getLayer ( Size index ) const

returns the layer data of the layer index

Exceptions

std::bad_cast exception if the current layer is not a LayerData1DBase

◆ getNonGravityDim()

const DimBase& getNonGravityDim ( ) const

Get the dimension on which gravity is currently not acting upon (the orthogonal axis; usually it's the X axis' unit)

◆ 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 ( ) const

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

◆ pushIntoDataRange() [1/2]

void pushIntoDataRange	(	PointXYType &	xy_unit,
		const int	layer_index
	)

inline

Pushes a data point back into the valid data range of the current layer area. Useful for annotation items which were mouse-dragged outside the range by the user.

Parameters

xy_unit	A pair (X and Y coordinate) with values in the units currently used on the axis
layer_index	The layer of the above data_point (to obtain the data range of the layer)

◆ pushIntoDataRange() [2/2]

void pushIntoDataRange	(	T &	data_point,
		const int	layer_index
	)

inline

Pushes a data point back into the valid data range of the current layer area. Useful for annotation items which were mouse-dragged outside the range by the user.

Template Parameters

T	A data point, e.g. Peak1D, which may be outside the data area

Parameters

data_point
layer_index	The layer of the above data_point (to obtain the data range of the layer)

Referenced by Annotation1DCaret< DataPoint >::ensureWithinDataRange(), and Annotation1DPeakItem< DataPoint >::ensureWithinDataRange().

◆ recalculatePercentageFactor_()

void recalculatePercentageFactor_ ( Size layer_index )

protected

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

◆ recalculateRanges_()

void recalculateRanges_ ( )

inlineoverrideprotectedvirtual

Recalculates the overall_data_range_ (by calling PlotCanvas::recalculateRanges_) plus the overall_data_range_1d_ (which only takes into account the current spec/chrom/.. of all layers)

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

Reimplemented from PlotCanvas.

References RangeManager< RangeBases >::clearRanges(), RangeManager< RangeBases >::extend(), RangeManager< RangeBases >::minSpanIfSingular(), PlotCanvas::recalculateRanges_(), and RangeManager< RangeBases >::scaleBy().

◆ removeLayer

void removeLayer ( Size layer_index )

overrideslot

◆ resetAlignment()

void resetAlignment ( )

Resets alignment_.

◆ resetZoom()

void resetZoom ( bool repaint = true )

inlineoverrideprotectedvirtual

Zooms fully out and resets the zoom stack.

Sets the visible area to the initial value, such that all data (for the current spec/chrom/...) is shown.

Parameters

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

Reimplemented from PlotCanvas.

References PlotCanvas::changeVisibleArea_().

◆ 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.

◆ setTextBox()

void setTextBox ( const QString & html )

Display a static text box on the top right.

◆ 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	(	const Precursor &	pc,
		const MSExperiment &	exp
	)

signal

Requests to display all spectra as DIA.

◆ showCurrentPeaksAsIonMobility

void showCurrentPeaksAsIonMobility ( const MSSpectrum & spec )

signal

Requests to display this spectrum (=frame) in ion mobility plot.

◆ translateBackward_()

void translateBackward_ ( )

overrideprotectedvirtual

Translation bound to the 'Down' key.

Reimplemented from PlotCanvas.

◆ translateForward_()

void translateForward_ ( )

overrideprotectedvirtual

Translation bound to the 'Up' key.

Reimplemented from PlotCanvas.

◆ 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

◆ updateScrollbars_()

void updateScrollbars_ ( )

overrideprotectedvirtual

Updates the scroll bars.

Updates the scrollbars after a change of the visible area.

Reimplemented from PlotCanvas.

◆ widgetToData() [1/2]

PointXYType widgetToData ( const QPoint & pos )

For convenience - calls widgetToData.

Referenced by Plot1DCanvas::widgetToDataDistance().

◆ widgetToData() [2/2]

PointXYType widgetToData	(	double	x,
		double	y
	)

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

◆ widgetToDataDistance()

PointXYType widgetToDataDistance	(	double	x,
		double	y
	)

inline

compute distance in data coordinates (unit axis as shown) when moving x/y pixel in chart/widget coordinates

References Plot1DCanvas::widgetToData().

Referenced by Annotation1DPeakItem< DataPoint >::draw().

◆ zoom_()

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

overrideprotectedvirtual

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

Reimplemented from PlotCanvas.

◆ zoomForward_()

void zoomForward_ ( )

overrideprotectedvirtual

Go forward in zoom history.

Reimplemented from PlotCanvas.

Friends And Related Function Documentation

◆ Painter1DChrom

friend class Painter1DChrom

friend

◆ Painter1DIonMobility

friend class Painter1DIonMobility

friend

◆ Painter1DPeak

friend class Painter1DPeak

friend

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_ = 0.0

protected

Stores the score of the last alignment.

◆ draw_interesting_MZs_

bool draw_interesting_MZs_ = false

protected

annotate interesting peaks with m/z's

◆ draw_modes_

std::vector<DrawModes> draw_modes_

protected

Draw modes (for each layer) - sticks or connected lines.

◆ gr_

Gravitator gr_

protected

handles pulling/pushing of points to the edges of the widget

◆ ion_ladder_visible_

bool ion_ladder_visible_ = true

protected

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

◆ measurement_start_point_px_

QPoint measurement_start_point_px_

protected

start point of "ruler" in pixel coordinates for measure mode

◆ mirror_mode_

bool mirror_mode_ = false

protected

Indicates whether this widget is currently in mirror mode.

◆ moving_annotations_

bool moving_annotations_ = false

protected

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

◆ overall_data_range_1d_

RangeType overall_data_range_1d_

protected

The data range (m/z, RT and intensity) of the current(!) spec/chrom for all layers.

◆ peak_penstyle_

std::vector<Qt::PenStyle> peak_penstyle_

protected

Draw style (for each layer)

◆ show_alignment_

bool show_alignment_ = false

protected

Indicates whether an alignment is currently visualized.

◆ text_box_content_

QTextDocument text_box_content_

protected

The text box in the upper left corner with the current data coordinates of the cursor.

◆ 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

Reimplemented QT events

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_() [1/3]

◆ changeVisibleArea_() [2/3]

◆ changeVisibleArea_() [3/3]

◆ changeVisibleAreaCommon_()

◆ contextMenuEvent()

◆ correctGravityAxisOfVisibleArea_()

◆ currentLayerParamtersChanged_

◆ dataToWidget() [1/3]

◆ dataToWidget() [2/3]

◆ dataToWidget() [3/3]

◆ dataToWidget_() [1/3]

◆ dataToWidget_() [2/3]

◆ dataToWidget_() [3/3]

◆ dataToWidgetDistance()

◆ drawAlignment_()

◆ drawCoordinates_()

◆ drawDeltas_()

◆ drawHighlightedPeak_()

◆ ensureAnnotationsWithinDataRange_()

◆ findPeakAtPosition_()

◆ finishAdding_()

◆ flipLayer()

◆ flippedLayersExist()

◆ getAlignedPeaksIndices()

◆ getAlignmentScore()

◆ getAlignmentSize()

◆ getCurrentLayer() [1/2]

◆ getCurrentLayer() [2/2]

◆ getDrawMode()

◆ getGravitator()

◆ getGravityDim()

◆ getLayer() [1/2]

◆ getLayer() [2/2]

◆ getNonGravityDim()

◆ horizontalScrollBarChange

◆ intensityModeChange_()

◆ isDrawInterestingMZs()

◆ isIonLadderVisible()

◆ keyPressEvent()

◆ mirrorModeActive()

◆ mouseMoveEvent()

◆ mousePressEvent()

◆ mouseReleaseEvent()

◆ paint()

◆ paintEvent()

◆ paintGridLines_()

◆ performAlignment()

◆ pushIntoDataRange() [1/2]

◆ pushIntoDataRange() [2/2]

◆ recalculatePercentageFactor_()

◆ recalculateRanges_()

◆ removeLayer

◆ resetAlignment()

◆ resetZoom()

◆ setCurrentLayerPeakPenStyle()

◆ setDrawInterestingMZs()