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void | showProjectionHorizontal (ExperimentSharedPtrType) |
| Sets the data for the horizontal projection. More...
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void | showProjectionVertical (ExperimentSharedPtrType) |
| Sets the data for the vertical projection. More...
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void | showProjectionInfo (int, double, double) |
| Shows the number of peaks and the intensity sum of the projection. More...
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void | toggleProjections () |
| Signal emitted when the projections are to be shown/hidden. More...
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void | showSpectrumAs1D (int index) |
| Requests to display the spectrum with index index in 1D. More...
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void | showSpectrumAs1D (std::vector< int, std::allocator< int > > indices) |
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void | showCurrentPeaksAs3D () |
| Requests to display all spectra in 3D plot. More...
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void | layerModficationChange (Size layer, bool modified) |
| Signal emitted whenever the modification status of a layer changes (editing and storing) More...
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void | layerActivated (QWidget *w) |
| Signal emitted whenever a new layer is activated within the current window. More...
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void | layerZoomChanged (QWidget *w) |
| Signal emitted whenever the zoom changed. More...
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void | visibleAreaChanged (DRange< 2 > area) |
| Change of the visible area. More...
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void | sendCursorStatus (double mz=-1.0, double rt=-1.0) |
| Emitted when the cursor position changes (for displaying e.g. in status bar) More...
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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...
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void | recalculateAxes () |
| Forces recalculation of axis ticks in the connected widget. More...
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void | updateVScrollbar (float, float, float, float) |
| Triggers the update of the vertical scrollbar. More...
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void | updateHScrollbar (float, float, float, float) |
| Triggers the update of the horizontal scrollbar. More...
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void | changeLegendVisibility () |
| Toggle axis legend visibility change. More...
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void | actionModeChange () |
| Emitted when the action mode changes. More...
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void | preferencesChange () |
| Emitted when the layer preferences have changed. More...
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| Spectrum2DCanvas (const Param &preferences, QWidget *parent=nullptr) |
| Default constructor. More...
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| ~Spectrum2DCanvas () override |
| Destructor. More...
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void | showCurrentLayerPreferences () override |
| Shows the preferences dialog of the active layer. More...
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void | saveCurrentLayer (bool visible) override |
| Saves the current layer data. More...
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void | mergeIntoLayer (Size i, FeatureMapSharedPtrType map) |
| Merges the features in map into the features layer i . More...
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void | mergeIntoLayer (Size i, ConsensusMapSharedPtrType map) |
| Merges the consensus features in map into the features layer i . More...
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void | mergeIntoLayer (Size i, std::vector< PeptideIdentification > &peptides) |
| Merges the peptide identifications in peptides into the peptide layer i . More...
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void | recalculateCurrentLayerDotGradient () |
| recalculates the dot gradient of the active layer More...
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| SpectrumCanvas (const Param &preferences, QWidget *parent=nullptr) |
| Default constructor. More...
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| ~SpectrumCanvas () override |
| Destructor. More...
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void | setSpectrumWidget (SpectrumWidget *widget) |
| Sets the spectrum widget. More...
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SpectrumWidget * | getSpectrumWidget () const |
| Returns the spectrum widget. More...
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Int | getActionMode () const |
| Returns the action mode. More...
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IntensityModes | getIntensityMode () const |
| Returns the intensity mode. More...
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void | setIntensityMode (IntensityModes mod) |
| Sets the intensity mode. More...
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bool | gridLinesShown () const |
| Returns if the grid is currently shown. More...
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const LayerData & | getLayer (Size index) const |
| returns the layer data with index index More...
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const LayerData & | getCurrentLayer () const |
| returns the layer data of the active layer More...
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Size | getCurrentLayerIndex () const |
| returns the index of the active layer More...
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LayerData & | getCurrentLayer () |
| returns the layer data of the active layer More...
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bool | getLayerFlag (LayerData::Flags f) const |
| returns a layer flag of the current layer More...
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void | setLayerFlag (LayerData::Flags f, bool value) |
| sets a layer flag of the current layer More...
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bool | getLayerFlag (Size layer, LayerData::Flags f) const |
| returns a layer flag of the layer layer More...
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void | setLayerFlag (Size layer, LayerData::Flags f, bool value) |
| sets a layer flag of the layer layer More...
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void | setLabel (LayerData::LabelType label) |
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const AreaType & | getVisibleArea () const |
| Returns the currently visible area. More...
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virtual void | setFilters (const DataFilters &filters) |
| Sets the filters applied to the data before drawing (for the current layer) More...
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bool | isMzToXAxis () |
| Returns the mapping of m/z to axes. More...
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void | mzToXAxis (bool mz_to_x_axis) |
| Sets the mapping of m/z to axes. More...
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bool | addLayer (std::vector< PeptideIdentification > &peptides, const String &filename="") |
| Add an identification data layer. More...
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float | getCurrentMinIntensity () const |
| Returns the minimum intensity of the active layer. More...
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float | getCurrentMaxIntensity () const |
| Returns the maximum intensity of the active layer. More...
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float | getMinIntensity (Size index) const |
| Returns the minimum intensity of the layer with index index . More...
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float | getMaxIntensity (Size index) const |
| Returns the maximum intensity of the layer with index index . More...
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void | setLayerName (Size i, const String &name) |
| Sets the name of layer i . More...
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String | getLayerName (Size i) |
| Gets the name of layer i . More...
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void | setCurrentLayerParameters (const Param ¶m) |
| Sets the parameters of the current layer. More...
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const DRange< 3 > & | getDataRange () |
| Returns the area which encloses all data points. More...
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double | getSnapFactor () |
| Returns the first intensity scaling factor for 'snap to maximum intensity mode'. More...
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double | getPercentageFactor () |
| Returns the percentage factor. More...
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virtual void | showMetaData (bool modifiable=false, Int index=-1) |
| Shows a dialog with the meta data. More...
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Size | getLayerCount () const |
| Returns the number of layers. More...
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Size | activeLayerIndex () const |
| Returns the index of the active layer. More...
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virtual void | activateLayer (Size layer_index)=0 |
| change the active layer (the one that is used for selecting and so on) More...
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virtual void | removeLayer (Size layer_index)=0 |
| removes the layer with index layer_index More...
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bool | addLayer (ExperimentSharedPtrType map, ODExperimentSharedPtrType od_map, const String &filename="") |
| Add a peak data layer. More...
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bool | addLayer (FeatureMapSharedPtrType map, const String &filename="") |
| Add a feature data layer. More...
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bool | addLayer (ConsensusMapSharedPtrType map, const String &filename="") |
| Add a consensus feature data layer. More...
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Public Member Functions inherited from DefaultParamHandler |
| DefaultParamHandler (const String &name) |
| Constructor with name that is displayed in error messages. More...
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| DefaultParamHandler (const DefaultParamHandler &rhs) |
| Copy constructor. More...
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virtual | ~DefaultParamHandler () |
| Destructor. More...
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virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| Assignment operator. More...
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virtual bool | operator== (const DefaultParamHandler &rhs) const |
| Equality operator. More...
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void | setParameters (const Param ¶m) |
| Sets the parameters. More...
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const Param & | getParameters () const |
| Non-mutable access to the parameters. More...
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const Param & | getDefaults () const |
| Non-mutable access to the default parameters. More...
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const String & | getName () const |
| Non-mutable access to the name. More...
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void | setName (const String &name) |
| Mutable access to the name. More...
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const std::vector< String > & | getSubsections () const |
| Non-mutable access to the registered subsections. More...
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bool | finishAdding_ () override |
| Method that is called when a new layer has been added. More...
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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...
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void | drawCoordinates_ (QPainter &painter, const PeakIndex &peak) |
| Draws the coordinates (or coordinate deltas) to the widget's upper left corner. More...
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void | drawDeltas_ (QPainter &painter, const PeakIndex &start, const PeakIndex &end) |
| Draws the coordinates (or coordinate deltas) to the widget's upper left corner. More...
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void | updateScrollbars_ () override |
| Updates the scroll bars. More...
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void | paintDots_ (Size layer_index, QPainter &p) |
| Paints individual peaks. More...
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void | paintAllIntensities_ (Size layer_index, double pen_width, QPainter &painter) |
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void | paintMaximumIntensities_ (Size layer_index, Size rt_pixel_count, Size mz_pixel_count, QPainter &p) |
| Paints maximum intensity of individual peaks. More...
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void | paintPrecursorPeaks_ (Size layer_index, QPainter &painter) |
| Paints the precursor peaks. More...
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void | paintFeatureData_ (Size layer_index, QPainter &p) |
| Paints feature data. More...
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void | paintTraceConvexHulls_ (Size layer_index, QPainter &p) |
| Paints convex hulls (one for each mass trace) of a features layer. More...
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void | paintFeatureConvexHulls_ (Size layer_index, QPainter &p) |
| Paints the convex hulls (one for each feature) of a features layer. More...
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void | paintIdentifications_ (Size layer_index, QPainter &p) |
| Paints peptide identifications (for idXML and unassigned peptides in featureXML). More...
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void | paintConsensusElements_ (Size layer_index, QPainter &p) |
| Paints the consensus elements of a consensus features layer. More...
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void | paintConsensusElement_ (Size layer_index, const ConsensusFeature &cf, QPainter &p, bool use_buffer) |
| Paints one consensus element of a consensus features layer. More...
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bool | isConsensusFeatureVisible_ (const ConsensusFeature &ce, Size layer_index) |
| checks if any element of a consensus feature is currently visible. More...
|
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void | paintConvexHulls_ (const std::vector< ConvexHull2D > &hulls, bool hasIdentifications, QPainter &p) |
| Paints convex hulls (one for each mass trace) for a single feature. More...
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void | intensityModeChange_ () override |
| This method is called whenever the intensity mode changes. Reimplement if you need to react on such changes. More...
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void | recalculateSnapFactor_ () override |
| Recalculates the intensity scaling factor for 'snap to maximum intensity mode'. More...
|
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Int | precalculatedColorIndex_ (float val, const MultiGradient &gradient, double snap_factor) |
| Returns the position on color gradient associated with given intensity. More...
|
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QColor | heightColor_ (float val, const MultiGradient &gradient, double snap_factor) |
| Returns the color associated with val for the gradient gradient . More...
|
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void | dataToWidget_ (double x, double y, QPoint &point) |
| Convert chart to widget coordinates. More...
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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...
|
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void | recalculateDotGradient_ (Size layer) |
| recalculates the dot gradient of a layer More...
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void | highlightPeak_ (QPainter &p, const PeakIndex &peak) |
| Highlights a single peak and prints coordinates to screen. More...
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PeakIndex | findNearestPeak_ (const QPoint &pos) |
| Returns the nearest peak to position pos . More...
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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...
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virtual void | translateVisibleArea_ (double mzShiftRel, double rtShiftRel) |
| translates the visible area by a given offset specified in fractions of current visible area More...
|
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void | translateLeft_ (Qt::KeyboardModifiers m) override |
| Translation bound to the 'Left' key. More...
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void | translateRight_ (Qt::KeyboardModifiers m) override |
| Translation bound to the 'Right' key. More...
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void | translateForward_ () override |
| Translation bound to the 'Up' key. More...
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void | translateBackward_ () override |
| Translation bound to the 'Down' key. More...
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void | finishContextMenu_ (QMenu *context_menu, QMenu *settings_menu) |
| Finishes context menu after customization to peaks, features or consensus features. More...
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void | mousePressEvent (QMouseEvent *e) override |
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void | mouseReleaseEvent (QMouseEvent *e) override |
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void | mouseMoveEvent (QMouseEvent *e) override |
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void | paintEvent (QPaintEvent *e) override |
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void | contextMenuEvent (QContextMenuEvent *e) override |
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void | keyPressEvent (QKeyEvent *e) override |
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void | keyReleaseEvent (QKeyEvent *e) override |
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void | mouseDoubleClickEvent (QMouseEvent *e) override |
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void | drawText_ (QPainter &painter, QStringList text) |
| Draws several lines of text to the upper right corner of the widget. More...
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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...
|
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LayerData & | getLayer_ (Size index) |
| Returns the layer with index index . More...
|
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LayerData & | getCurrentLayer_ () |
| Returns the currently active layer. More...
|
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virtual void | changeVisibleArea_ (const AreaType &new_area, bool repaint=true, bool add_to_stack=false) |
| Sets the visible area. More...
|
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PointType | widgetToData_ (double x, double y) |
| Convert widget to chart coordinates. More...
|
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PointType | widgetToData_ (const QPoint &pos) |
| Calls widgetToData_ with x and y position of pos . More...
|
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void | dataToWidget_ (double x, double y, QPoint &point) |
| Convert chart to widget coordinates. More...
|
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virtual void | paintGridLines_ (QPainter &painter) |
| Helper function to paint grid lines. More...
|
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void | recalculateRanges_ (UInt mz_dim, UInt rt_dim, UInt it_dim) |
| Recalculates the overall_data_range_. More...
|
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virtual void | update_ (const char *caller_name) |
| Updates the displayed data. More...
|
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void | modificationStatus_ (Size layer_index, bool modified) |
| Takes all actions necessary when the modification status of a layer changes (signals etc.) More...
|
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void | adjustBuffer_ () |
| Changes the size of the paint buffer to the currently required size. More...
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void | addDataProcessing_ (PeakMap &map, DataProcessing::ProcessingAction action) const |
| Data processing setter for peak maps. More...
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void | resizeEvent (QResizeEvent *e) override |
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void | wheelEvent (QWheelEvent *e) override |
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void | keyPressEvent (QKeyEvent *e) override |
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void | keyReleaseEvent (QKeyEvent *e) override |
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void | focusOutEvent (QFocusEvent *e) override |
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void | leaveEvent (QEvent *e) override |
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void | enterEvent (QEvent *e) override |
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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...
|
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void | zoomBack_ () |
| Go backward in zoom history. More...
|
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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...
|
|
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...
|
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void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. More...
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|
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:
Name | Type | Default | Restrictions | Description |
default_path |
string | . |
| Default path for loading/storing data. |
background_color |
string | @#ffffff |
| Background color. |
interpolation_steps |
int | 1000 |
min: 1 max: 1000 | Number of interpolation steps for peak gradient pre-calculation. |
mapping_of_mz_to |
string | y_axis |
x_axis, y_axis | Determines which axis is the m/z axis. |
dot:gradient |
string | Linear|0,@#eeeeee;1,@#ffea00;6,@#ff0000;14,@#aa00ff;23,@#5500ff;100,@#000000 |
| Multi-color gradient for peaks. |
dot:feature_icon |
string | circle |
diamond, square, circle, triangle | Icon used for features and consensus features. |
dot:feature_icon_size |
int | 4 |
min: 1 max: 999 | Icon size used for features and consensus features. |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
- Improvement:
- Add RT interpolation mode for high zoom in 2D View (Hiwi)
- Improvement:
- Snap also to min intensity (Hiwi)