OpenMS  2.6.0
Public Slots | Signals | Public Member Functions | Protected Slots | Protected Member Functions | List of all members
Spectrum2DCanvas Class Reference

Canvas for 2D-visualization of peak map, feature map and consensus map data. More...

#include <OpenMS/VISUAL/Spectrum2DCanvas.h>

Inheritance diagram for Spectrum2DCanvas:
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Collaboration diagram for Spectrum2DCanvas:
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Public Slots

void activateLayer (Size layer_index) override
 
void removeLayer (Size layer_index) override
 
void updateLayer (Size i) override
 
void horizontalScrollBarChange (int value) override
 
void verticalScrollBarChange (int value) override
 
void updateProjections ()
 Updates the projection data and emits some related signals. More...
 
- Public Slots inherited from SpectrumCanvas
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 showProjectionHorizontal (ExperimentSharedPtrType)
 Sets the data for the horizontal projection. More...
 
void showProjectionVertical (ExperimentSharedPtrType)
 Sets the data for the vertical projection. More...
 
void showProjectionInfo (int, double, double)
 Shows the number of peaks and the intensity sum of the projection. More...
 
void toggleProjections ()
 Signal emitted when the projections are to be shown/hidden. More...
 
void showSpectrumAs1D (int index)
 Requests to display the spectrum with index index in 1D. More...
 
void showSpectrumAs1D (std::vector< int, std::allocator< int > > indices)
 
void showCurrentPeaksAs3D ()
 Requests to display all spectra in 3D plot. More...
 
- Signals inherited from SpectrumCanvas
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

 Spectrum2DCanvas (const Param &preferences, QWidget *parent=nullptr)
 Default constructor. More...
 
 ~Spectrum2DCanvas () override
 Destructor. More...
 
void showCurrentLayerPreferences () override
 Shows the preferences dialog of the active layer. More...
 
void saveCurrentLayer (bool visible) override
 Saves the current layer data. More...
 
void mergeIntoLayer (Size i, FeatureMapSharedPtrType map)
 Merges the features in map into the features layer i. More...
 
void mergeIntoLayer (Size i, ConsensusMapSharedPtrType map)
 Merges the consensus features in map into the features layer i. More...
 
void mergeIntoLayer (Size i, std::vector< PeptideIdentification > &peptides)
 Merges the peptide identifications in peptides into the peptide layer i. More...
 
void recalculateCurrentLayerDotGradient ()
 recalculates the dot gradient of the active layer More...
 
- Public Member Functions inherited from SpectrumCanvas
 SpectrumCanvas (const Param &preferences, QWidget *parent=nullptr)
 Default constructor. More...
 
 ~SpectrumCanvas () override
 Destructor. More...
 
void setSpectrumWidget (SpectrumWidget *widget)
 Sets the spectrum widget. More...
 
SpectrumWidgetgetSpectrumWidget () 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 LayerDatagetLayer (Size index) const
 returns the layer data with index index More...
 
const LayerDatagetCurrentLayer () const
 returns the layer data of the active layer More...
 
Size getCurrentLayerIndex () const
 returns the index of the active layer More...
 
LayerDatagetCurrentLayer ()
 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 AreaTypegetVisibleArea () 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...
 
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, 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 DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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 currentLayerParametersChanged_ ()
 Reacts on changed layer parameters. More...
 
- Protected Slots inherited from SpectrumCanvas
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...
 
bool collectFragmentScansInArea (double rt_min, double rt_max, double mz_min, double mz_max, QAction *a, QMenu *msn_scans, QMenu *msn_meta)
 Collects fragment ion scans in the indicated RT/mz area and adds them to the indicated action. 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...
 
- Protected Member Functions inherited from SpectrumCanvas
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
 
virtual void changeVisibleArea_ (const AreaType &new_area, bool repaint=true, bool add_to_stack=false)
 Sets the visible area. More...
 
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...
 
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...
 
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="")
 
LayerDatagetLayer_ (Size index)
 Returns the layer with index index. More...
 
LayerDatagetCurrentLayer_ ()
 Returns the currently active layer. 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...
 

Reimplemented QT events

ExperimentType projection_mz_
 m/z projection data More...
 
ExperimentType projection_rt_
 RT projection data. More...
 
PeakIndex selected_peak_
 the nearest peak/feature to the mouse cursor More...
 
PeakIndex measurement_start_
 start peak/feature of measuring mode More...
 
MultiGradient linear_gradient_
 stores the linear color gradient for non-log modes More...
 
double pen_size_min_
 minimum number of pixels for one data point More...
 
double pen_size_max_
 maximum number of pixels for one data point More...
 
double canvas_coverage_min_
 minimum coverage of the canvas required; if lower, points are upscaled in size More...
 
void mousePressEvent (QMouseEvent *e) override
 
void mouseReleaseEvent (QMouseEvent *e) override
 
void mouseMoveEvent (QMouseEvent *e) override
 
void paintEvent (QPaintEvent *e) override
 
void contextMenuEvent (QContextMenuEvent *e) override
 
void keyPressEvent (QKeyEvent *e) override
 
void keyReleaseEvent (QKeyEvent *e) override
 
void mouseDoubleClickEvent (QMouseEvent *e) override
 
void updateScrollbars_ () override
 Updates the scroll bars. More...
 
void paintDots_ (Size layer_index, QPainter &p)
 Paints individual peaks. More...
 
void paintAllIntensities_ (Size layer_index, double pen_width, QPainter &painter)
 
void paintMaximumIntensities_ (Size layer_index, Size rt_pixel_count, Size mz_pixel_count, QPainter &p)
 Paints maximum intensity of individual peaks. More...
 
void paintPrecursorPeaks_ (Size layer_index, QPainter &painter)
 Paints the precursor peaks. More...
 
void paintFeatureData_ (Size layer_index, QPainter &p)
 Paints feature data. More...
 
void paintTraceConvexHulls_ (Size layer_index, QPainter &p)
 Paints convex hulls (one for each mass trace) of a features layer. More...
 
void paintFeatureConvexHulls_ (Size layer_index, QPainter &p)
 Paints the convex hulls (one for each feature) of a features layer. More...
 
void paintIdentifications_ (Size layer_index, QPainter &p)
 Paints peptide identifications (for idXML and unassigned peptides in featureXML). More...
 
void paintConsensusElements_ (Size layer_index, QPainter &p)
 Paints the consensus elements of a consensus features layer. More...
 
void paintConsensusElement_ (Size layer_index, const ConsensusFeature &cf, QPainter &p, bool use_buffer)
 Paints one consensus element of a consensus features layer. More...
 
bool isConsensusFeatureVisible_ (const ConsensusFeature &ce, Size layer_index)
 checks if any element of a consensus feature is currently visible. More...
 
void paintConvexHulls_ (const std::vector< ConvexHull2D > &hulls, bool hasIdentifications, QPainter &p)
 Paints convex hulls (one for each mass trace) for a single feature. More...
 
void intensityModeChange_ () override
 This method is called whenever the intensity mode changes. Reimplement if you need to react on such changes. More...
 
void recalculateSnapFactor_ () override
 Recalculates the intensity scaling factor for 'snap to maximum intensity mode'. More...
 
Int precalculatedColorIndex_ (float val, const MultiGradient &gradient, double snap_factor)
 Returns the position on color gradient associated with given intensity. More...
 
QColor heightColor_ (float val, const MultiGradient &gradient, double snap_factor)
 Returns the color associated with val for the gradient gradient. More...
 
void dataToWidget_ (double x, double y, QPoint &point)
 Convert chart to widget coordinates. More...
 
double adaptPenScaling_ (double ratio_data2pixel, double &pen_size) const
 For a certain dimension: computes the size a data point would need, such that the image reaches a certain coverage. More...
 
void recalculateDotGradient_ (Size layer)
 recalculates the dot gradient of a layer More...
 
void highlightPeak_ (QPainter &p, const PeakIndex &peak)
 Highlights a single peak and prints coordinates to screen. More...
 
PeakIndex findNearestPeak_ (const QPoint &pos)
 Returns the nearest peak to position pos. More...
 
void paintIcon_ (const QPoint &pos, const QRgb &color, const String &icon, Size s, QPainter &p) const
 Paints a peak icon for feature and consensus feature peaks. More...
 
virtual void translateVisibleArea_ (double mzShiftRel, double rtShiftRel)
 translates the visible area by a given offset specified in fractions of current visible area 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 finishContextMenu_ (QMenu *context_menu, QMenu *settings_menu)
 Finishes context menu after customization to peaks, features or consensus features. More...
 
 Spectrum2DCanvas ()
 Default C'tor hidden. More...
 

Additional Inherited Members

- Public Types inherited from SpectrumCanvas
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::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...
 
- 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...
 
- Protected Attributes inherited from SpectrumCanvas
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< LayerDatalayers_
 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< AreaTypezoom_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...
 
SpectrumWidgetspectrum_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< doublesnap_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< Stringsubsections_
 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 2D-visualization of peak map, feature map and consensus map data.

This widget displays a 2D representation of a set of peaks, features or consensus elements.

The example image shows Spectrum2DCanvas displaying a peak layer and a feature layer.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
default_path string.  Default path for loading/storing data.
background_color string@#ffffff  Background color.
interpolation_steps int1000 min: 1 max: 1000Number of interpolation steps for peak gradient pre-calculation.
mapping_of_mz_to stringy_axis x_axis, y_axisDetermines which axis is the m/z axis.
dot:gradient stringLinear|0,@#eeeeee;1,@#ffea00;6,@#ff0000;14,@#aa00ff;23,@#5500ff;100,@#000000  Multi-color gradient for peaks.
dot:feature_icon stringcircle diamond, square, circle, triangleIcon used for features and consensus features.
dot:feature_icon_size int4 min: 1 max: 999Icon size used for features and consensus features.

Note:
Improvement:
Add RT interpolation mode for high zoom in 2D View (Hiwi)
Improvement:
Snap also to min intensity (Hiwi)

Constructor & Destructor Documentation

◆ Spectrum2DCanvas() [1/2]

Spectrum2DCanvas ( const Param preferences,
QWidget parent = nullptr 
)

Default constructor.

◆ ~Spectrum2DCanvas()

~Spectrum2DCanvas ( )
override

Destructor.

◆ Spectrum2DCanvas() [2/2]

Spectrum2DCanvas ( )
private

Default C'tor hidden.

Member Function Documentation

◆ activateLayer

void activateLayer ( Size  layer_index)
overrideslot

◆ adaptPenScaling_()

double adaptPenScaling_ ( double  ratio_data2pixel,
double pen_size 
) const
protected

For a certain dimension: computes the size a data point would need, such that the image reaches a certain coverage.

Internally, this function makes use of the members 'canvas_coverage_min_' (giving the fraction (e.g. 20%) of area which should be covered by data) and 'pen_size_max_' (maximum allowed number of pixels per data point).

Parameters
ratio_data2pixelThe current ratio of #data points vs. # pixels of image
pen_sizeIn/Out param: gives the initial pen size, and is increased (up to MAX_PEN_SIZE) to reach desired coverage given by 'canvas_coverage_min_'
Returns
The factor by which @pen_size increased (gives a hint of how many data points should be merged to avoid overplotting)

◆ collectFragmentScansInArea()

bool collectFragmentScansInArea ( double  rt_min,
double  rt_max,
double  mz_min,
double  mz_max,
QAction *  a,
QMenu *  msn_scans,
QMenu *  msn_meta 
)
protected

Collects fragment ion scans in the indicated RT/mz area and adds them to the indicated action.

◆ contextMenuEvent()

void contextMenuEvent ( QContextMenuEvent *  e)
overrideprotected

◆ currentLayerParametersChanged_

void currentLayerParametersChanged_ ( )
protectedslot

Reacts on changed layer parameters.

◆ dataToWidget_()

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

Convert chart to widget coordinates.

Translates chart coordinates to widget coordinates.

Parameters
xthe chart coordinate x
ythe chart coordinate y
pointreturned widget coordinates

◆ 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.

◆ findNearestPeak_()

PeakIndex findNearestPeak_ ( const QPoint &  pos)
protected

Returns the nearest peak to position pos.

◆ finishAdding_()

bool finishAdding_ ( )
overrideprotectedvirtual

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

Implements SpectrumCanvas.

◆ finishContextMenu_()

void finishContextMenu_ ( QMenu *  context_menu,
QMenu *  settings_menu 
)
protected

Finishes context menu after customization to peaks, features or consensus features.

◆ heightColor_()

QColor heightColor_ ( float  val,
const MultiGradient gradient,
double  snap_factor 
)
inlineprotected

Returns the color associated with val for the gradient gradient.

Takes intensity modes into account.

References MultiGradient::precalculatedColorByIndex().

◆ highlightPeak_()

void highlightPeak_ ( QPainter &  p,
const PeakIndex peak 
)
protected

Highlights a single peak and prints coordinates to screen.

◆ 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 SpectrumCanvas.

◆ isConsensusFeatureVisible_()

bool isConsensusFeatureVisible_ ( const ConsensusFeature ce,
Size  layer_index 
)
protected

checks if any element of a consensus feature is currently visible.

Parameters
layer_indexIndex of the layer.
ceThe ConsensusFeature that needs checking

◆ keyPressEvent()

void keyPressEvent ( QKeyEvent *  e)
overrideprotected

◆ keyReleaseEvent()

void keyReleaseEvent ( QKeyEvent *  e)
overrideprotected

◆ mergeIntoLayer() [1/3]

void mergeIntoLayer ( Size  i,
ConsensusMapSharedPtrType  map 
)

Merges the consensus features in map into the features layer i.

◆ mergeIntoLayer() [2/3]

void mergeIntoLayer ( Size  i,
FeatureMapSharedPtrType  map 
)

Merges the features in map into the features layer i.

Referenced by TOPPViewBase::addData().

◆ mergeIntoLayer() [3/3]

void mergeIntoLayer ( Size  i,
std::vector< PeptideIdentification > &  peptides 
)

Merges the peptide identifications in peptides into the peptide layer i.

◆ mouseDoubleClickEvent()

void mouseDoubleClickEvent ( QMouseEvent *  e)
overrideprotected

◆ mouseMoveEvent()

void mouseMoveEvent ( QMouseEvent *  e)
overrideprotected

◆ mousePressEvent()

void mousePressEvent ( QMouseEvent *  e)
overrideprotected

◆ mouseReleaseEvent()

void mouseReleaseEvent ( QMouseEvent *  e)
overrideprotected

◆ paintAllIntensities_()

void paintAllIntensities_ ( Size  layer_index,
double  pen_width,
QPainter &  painter 
)
protected

◆ paintConsensusElement_()

void paintConsensusElement_ ( Size  layer_index,
const ConsensusFeature cf,
QPainter &  p,
bool  use_buffer 
)
protected

Paints one consensus element of a consensus features layer.

Parameters
layer_indexIndex of the layer.
cfReference to the feature to be painted.
pThe QPainter to paint on.
use_bufferFlag to switch between painting on the buffer and screen.

◆ paintConsensusElements_()

void paintConsensusElements_ ( Size  layer_index,
QPainter &  p 
)
protected

Paints the consensus elements of a consensus features layer.

Parameters
layer_indexIndex of the layer.
pThe QPainter to paint on.

◆ paintConvexHulls_()

void paintConvexHulls_ ( const std::vector< ConvexHull2D > &  hulls,
bool  hasIdentifications,
QPainter &  p 
)
protected

Paints convex hulls (one for each mass trace) for a single feature.

Parameters
hullsReference to convex hull vector.
pThe QPainter to paint on.

◆ paintDots_()

void paintDots_ ( Size  layer_index,
QPainter &  p 
)
protected

Paints individual peaks.

Calls different painting methods depending on the layer type and the density of displayed peaks

Parameters
layer_indexThe index of the layer.
pThe QPainter to paint on.

◆ paintEvent()

void paintEvent ( QPaintEvent *  e)
overrideprotected

◆ paintFeatureConvexHulls_()

void paintFeatureConvexHulls_ ( Size  layer_index,
QPainter &  p 
)
protected

Paints the convex hulls (one for each feature) of a features layer.

Parameters
layer_indexIndex of the layer.
pThe QPainter to paint on.

◆ paintFeatureData_()

void paintFeatureData_ ( Size  layer_index,
QPainter &  p 
)
protected

Paints feature data.

Parameters
layer_indexThe index of the layer.
pThe QPainter to paint on.

◆ paintIcon_()

void paintIcon_ ( const QPoint &  pos,
const QRgb &  color,
const String icon,
Size  s,
QPainter &  p 
) const
protected

Paints a peak icon for feature and consensus feature peaks.

◆ paintIdentifications_()

void paintIdentifications_ ( Size  layer_index,
QPainter &  p 
)
protected

Paints peptide identifications (for idXML and unassigned peptides in featureXML).

Parameters
layer_indexIndex of the layer.
pThe QPainter to paint on.

◆ paintMaximumIntensities_()

void paintMaximumIntensities_ ( Size  layer_index,
Size  rt_pixel_count,
Size  mz_pixel_count,
QPainter &  p 
)
protected

Paints maximum intensity of individual peaks.

Paints the peaks as small ellipses. The peaks are colored according to the selected dot gradient.

Parameters
layer_indexThe index of the layer.
rt_pixel_count
mz_pixel_count
pThe QPainter to paint on.

◆ paintPrecursorPeaks_()

void paintPrecursorPeaks_ ( Size  layer_index,
QPainter &  painter 
)
protected

Paints the precursor peaks.

Parameters
layer_indexThe index of the layer.
painterThe QPainter to paint on.

◆ paintTraceConvexHulls_()

void paintTraceConvexHulls_ ( Size  layer_index,
QPainter &  p 
)
protected

Paints convex hulls (one for each mass trace) of a features layer.

Parameters
layer_indexIndex of the layer.
pThe QPainter to paint on.

◆ precalculatedColorIndex_()

Int precalculatedColorIndex_ ( float  val,
const MultiGradient gradient,
double  snap_factor 
)
inlineprotected

Returns the position on color gradient associated with given intensity.

Takes intensity modes into account.

References OpenMS::IM_NONE, and MultiGradient::precalculatedColorIndex().

◆ recalculateCurrentLayerDotGradient()

void recalculateCurrentLayerDotGradient ( )

recalculates the dot gradient of the active layer

◆ recalculateDotGradient_()

void recalculateDotGradient_ ( Size  layer)
protected

recalculates the dot gradient of a layer

◆ recalculateSnapFactor_()

void recalculateSnapFactor_ ( )
overrideprotectedvirtual

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

See also
snap_factors_

Reimplemented from SpectrumCanvas.

◆ removeLayer

void removeLayer ( Size  layer_index)
overrideslot

◆ saveCurrentLayer()

void saveCurrentLayer ( bool  visible)
overridevirtual

Saves the current layer data.

Parameters
visibleIf true, only the visible data is stored. Otherwise the whole data is stored.

Implements SpectrumCanvas.

◆ showCurrentLayerPreferences()

void showCurrentLayerPreferences ( )
overridevirtual

Shows the preferences dialog of the active layer.

Implements SpectrumCanvas.

◆ showCurrentPeaksAs3D

void showCurrentPeaksAs3D ( )
signal

Requests to display all spectra in 3D plot.

◆ showProjectionHorizontal

void showProjectionHorizontal ( ExperimentSharedPtrType  )
signal

Sets the data for the horizontal projection.

◆ showProjectionInfo

void showProjectionInfo ( int  ,
double  ,
double   
)
signal

Shows the number of peaks and the intensity sum of the projection.

◆ showProjectionVertical

void showProjectionVertical ( ExperimentSharedPtrType  )
signal

Sets the data for the vertical projection.

◆ showSpectrumAs1D [1/2]

void showSpectrumAs1D ( int  index)
signal

Requests to display the spectrum with index index in 1D.

◆ showSpectrumAs1D [2/2]

void showSpectrumAs1D ( std::vector< int, std::allocator< int > >  indices)
signal

◆ toggleProjections

void toggleProjections ( )
signal

Signal emitted when the projections are to be shown/hidden.

◆ translateBackward_()

void translateBackward_ ( )
overrideprotectedvirtual

Translation bound to the 'Down' key.

Reimplemented from SpectrumCanvas.

◆ translateForward_()

void translateForward_ ( )
overrideprotectedvirtual

Translation bound to the 'Up' key.

Reimplemented from SpectrumCanvas.

◆ translateLeft_()

void translateLeft_ ( Qt::KeyboardModifiers  m)
overrideprotectedvirtual

Translation bound to the 'Left' key.

Reimplemented from SpectrumCanvas.

◆ translateRight_()

void translateRight_ ( Qt::KeyboardModifiers  m)
overrideprotectedvirtual

Translation bound to the 'Right' key.

Reimplemented from SpectrumCanvas.

◆ translateVisibleArea_()

virtual void translateVisibleArea_ ( double  mzShiftRel,
double  rtShiftRel 
)
protectedvirtual

translates the visible area by a given offset specified in fractions of current visible area

◆ updateLayer

void updateLayer ( Size  i)
overrideslot

◆ updateProjections

void updateProjections ( )
slot

Updates the projection data and emits some related signals.

Emitted signals are showProjectionHorizontal(ExperimentSharedPtrType, Spectrum1DCanvas::DrawModes, SpectrumCanvas::IntensityModes) and showProjectionVertical(ExperimentSharedPtrType, Spectrum1DCanvas::DrawModes, SpectrumCanvas::IntensityModes).

See also
projection_mz_
projection_rt_

◆ updateScrollbars_()

void updateScrollbars_ ( )
overrideprotectedvirtual

Updates the scroll bars.

Updates the scrollbars after a change of the visible area.

Reimplemented from SpectrumCanvas.

◆ verticalScrollBarChange

void verticalScrollBarChange ( int  value)
overrideslot

Member Data Documentation

◆ canvas_coverage_min_

double canvas_coverage_min_
protected

minimum coverage of the canvas required; if lower, points are upscaled in size

◆ linear_gradient_

MultiGradient linear_gradient_
protected

stores the linear color gradient for non-log modes

◆ measurement_start_

PeakIndex measurement_start_
protected

start peak/feature of measuring mode

◆ pen_size_max_

double pen_size_max_
protected

maximum number of pixels for one data point

◆ pen_size_min_

double pen_size_min_
protected

minimum number of pixels for one data point

◆ projection_mz_

ExperimentType projection_mz_
protected

m/z projection data

◆ projection_rt_

ExperimentType projection_rt_
protected

RT projection data.

◆ selected_peak_

PeakIndex selected_peak_
protected

the nearest peak/feature to the mouse cursor