|
| void | showProjectionHorizontal (ExperimentSharedPtrType, Spectrum1DCanvas::DrawModes) |
| | Sets the data for the horizontal projection. More...
|
| |
| void | showProjectionVertical (ExperimentSharedPtrType, Spectrum1DCanvas::DrawModes) |
| | 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...
|
| |
| 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...
|
| |
|
| | Spectrum2DCanvas (const Param &preferences, QWidget *parent=0) |
| | Default constructor. More...
|
| |
| | ~Spectrum2DCanvas () |
| | Destructor. More...
|
| |
| virtual void | showCurrentLayerPreferences () |
| | Shows the preferences dialog of the active layer. More...
|
| |
| virtual void | saveCurrentLayer (bool visible) |
| | 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...
|
| |
| | SpectrumCanvas (const Param &preferences, QWidget *parent=0) |
| | Default constructor. More...
|
| |
| virtual | ~SpectrumCanvas () |
| | Destructor. More...
|
| |
| void | setSpectrumWidget (SpectrumWidget *widget) |
| | Sets the spectrum widget. More...
|
| |
| SpectrumWidget * | getSpectrumWidget () const |
| | Returns the spectrum widget. More...
|
| |
| Int | getActionMode () const |
| | Returns the action mode. More...
|
| |
| Int | getIntensityMode () const |
| | Returns the intensity mode. More...
|
| |
| void | setIntensityMode (IntensityModes mod) |
| | Sets the intensity mode. More...
|
| |
| bool | gridLinesShown () const |
| | Returns if the grid is currently shown. More...
|
| |
| const LayerData & | getLayer (Size index) const |
| | returns the layer data with index index More...
|
| |
| const LayerData & | getCurrentLayer () const |
| | returns the layer data of the active layer More...
|
| |
| Size | getCurrentLayerIndex () const |
| | returns the index of the active layer More...
|
| |
| LayerData & | getCurrentLayer () |
| | returns the layer data of the active layer More...
|
| |
| bool | getLayerFlag (LayerData::Flags f) const |
| | returns a layer flag of the current layer More...
|
| |
| void | setLayerFlag (LayerData::Flags f, bool value) |
| | sets a layer flag of the current layer More...
|
| |
| bool | getLayerFlag (Size layer, LayerData::Flags f) const |
| | returns a layer flag of the layer layer More...
|
| |
| void | setLayerFlag (Size layer, LayerData::Flags f, bool value) |
| | sets a layer flag of the layer layer More...
|
| |
| void | setLabel (LayerData::LabelType label) |
| |
| const AreaType & | getVisibleArea () const |
| | Returns the currently visible area. More...
|
| |
| virtual void | setFilters (const DataFilters &filters) |
| | Sets the filters applied to the data before drawing (for the current layer) More...
|
| |
| bool | isMzToXAxis () |
| | Returns the mapping of m/z to axes. More...
|
| |
| void | mzToXAxis (bool mz_to_x_axis) |
| | Sets the mapping of m/z to axes. More...
|
| |
| bool | addLayer (std::vector< PeptideIdentification > &peptides, const String &filename="") |
| | Add an identification data layer. More...
|
| |
| Real | getCurrentMinIntensity () const |
| | Returns the minimum intensity of the active layer. More...
|
| |
| Real | getCurrentMaxIntensity () const |
| | Returns the maximum intensity of the active layer. More...
|
| |
| Real | getMinIntensity (Size index) const |
| | Returns the minimum intensity of the layer with index index. More...
|
| |
| Real | 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 ¶m) |
| | Sets the parameters of the current layer. More...
|
| |
| const DRange< 3 > & | getDataRange () |
| | Returns the area which encloses all data points. More...
|
| |
| DoubleReal | getSnapFactor () |
| | Returns the first intensity scaling factor for 'snap to maximum intensity mode'. More...
|
| |
| DoubleReal | getPercentageFactor () |
| | Returns the percentage factor. More...
|
| |
| virtual void | showMetaData (bool modifiable=false, Int index=-1) |
| | Shows a dialog with the meta data. 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, const String &filename="") |
| | Add a peak data layer. More...
|
| |
| bool | addLayer (FeatureMapSharedPtrType map, const String &filename="") |
| | Add a feature data layer. More...
|
| |
| bool | addLayer (ConsensusMapSharedPtrType map, const String &filename="") |
| | Add a consensus feature data layer. More...
|
| |
Public Member Functions inherited from DefaultParamHandler |
| | DefaultParamHandler (const String &name) |
| | Constructor with name that is displayed in error messages. More...
|
| |
| | DefaultParamHandler (const DefaultParamHandler &rhs) |
| | Copy constructor. More...
|
| |
| virtual | ~DefaultParamHandler () |
| | Destructor. More...
|
| |
| virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| | Assignment operator. More...
|
| |
| virtual bool | operator== (const DefaultParamHandler &rhs) const |
| | Equality operator. More...
|
| |
| void | setParameters (const Param ¶m) |
| | 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...
|
| |
|
| bool | finishAdding_ () |
| | 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...
|
| |
| virtual void | updateScrollbars_ () |
| | Updates the scroll bars. More...
|
| |
| void | paintDots_ (Size layer_index, QPainter &p) |
| | Paints individual peaks. More...
|
| |
| void | paintAllIntensities_ (Size layer_index, DoubleReal 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...
|
| |
| virtual void | intensityModeChange_ () |
| | This method is called whenever the intensity mode changes. Reimplement if you need to react on such changes. More...
|
| |
| virtual void | recalculateSnapFactor_ () |
| | REcalculates the intensity scaling factor for 'snap to maximum intensity mode'. More...
|
| |
| Int | precalculatedColorIndex_ (Real val, const MultiGradient &gradient, DoubleReal snap_factor) |
| | Returns the position on color gradient associated with given intensity. More...
|
| |
| QColor | heightColor_ (Real val, const MultiGradient &gradient, DoubleReal snap_factor) |
| | Returns the color associated with val for the gradient gradient. More...
|
| |
| void | dataToWidget_ (DoubleReal x, DoubleReal y, QPoint &point) |
| | Convert chart to widget coordinates. 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_ (DoubleReal mzShiftRel, DoubleReal rtShiftRel) |
| | translates the visible area by a given offset specified in fractions of current visible area More...
|
| |
| virtual void | translateLeft_ () |
| | Translation bound to the 'Left' key. More...
|
| |
| virtual void | translateRight_ () |
| | Translation bound to the 'Rightt' key. More...
|
| |
| virtual void | translateForward_ () |
| | Translation bound to the 'Up' key. More...
|
| |
| virtual void | translateBackward_ () |
| | 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...
|
| |
|
| void | mousePressEvent (QMouseEvent *e) |
| |
| void | mouseReleaseEvent (QMouseEvent *e) |
| |
| void | mouseMoveEvent (QMouseEvent *e) |
| |
| void | paintEvent (QPaintEvent *e) |
| |
| void | contextMenuEvent (QContextMenuEvent *e) |
| |
| void | keyPressEvent (QKeyEvent *e) |
| |
| void | keyReleaseEvent (QKeyEvent *e) |
| |
| void | mouseDoubleClickEvent (QMouseEvent *e) |
| |
| void | drawText_ (QPainter &painter, QStringList text) |
| | Draws several lines of text to the upper right corner of the widget. More...
|
| |
| DoubleReal | 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...
|
| |
| LayerData & | getLayer_ (Size index) |
| | Returns the layer with index index. More...
|
| |
| LayerData & | getCurrentLayer_ () |
| | Returns the currently active layer. More...
|
| |
| ExperimentSharedPtrType | currentPeakData_ () |
| | Returns the currently active layer (mutable) More...
|
| |
| virtual void | changeVisibleArea_ (const AreaType &new_area, bool repaint=true, bool add_to_stack=false) |
| | Sets the visible area. More...
|
| |
| PointType | widgetToData_ (DoubleReal x, DoubleReal y) |
| | Convert widget to chart coordinates. More...
|
| |
| PointType | widgetToData_ (const QPoint &pos) |
| | Calls widgetToData_ with x and y position of pos. More...
|
| |
| void | dataToWidget_ (DoubleReal x, DoubleReal 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 diplayed 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...
|
| |
| template<typename PeakType > |
| void | addDataProcessing_ (MSExperiment< PeakType > &map, DataProcessing::ProcessingAction action) const |
| | Data processing setter for peak maps. More...
|
| |
| void | resizeEvent (QResizeEvent *e) |
| |
| void | wheelEvent (QWheelEvent *e) |
| |
| void | keyPressEvent (QKeyEvent *e) |
| |
| void | keyReleaseEvent (QKeyEvent *e) |
| |
| void | focusOutEvent (QFocusEvent *e) |
| |
| void | leaveEvent (QEvent *e) |
| |
| void | enterEvent (QEvent *e) |
| |
| 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...
|
| |
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...
|
| |
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 interploation steps for peak gradient precalculation. |
| 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)