| OpenMS 2.5.0

Public Slots | Signals | Public Member Functions | Protected Slots | Protected Member Functions | Protected Attributes | Private Member Functions | List of all members
Spectrum2DCanvas Class Reference
Visual » Spectrum visualization widgets

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

`#include <OpenMS/VISUAL/Spectrum2DCanvas.h>`

Inheritance diagram for Spectrum2DCanvas:

## 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...
SpectrumWidget * | getSpectrumWidget () const
| Returns the spectrum widget. More...
Int | getActionMode () const
| Returns the action mode. More...
IntensityModes | getIntensityMode () const
| Returns the intensity mode. More...
void | setIntensityMode (IntensityModes mod)
| Sets the intensity mode. More...
bool | gridLinesShown () const
| Returns if the grid is currently shown. More...
const LayerData & | getLayer (Size index) const
| returns the layer data with index `index` More...
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...
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...
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...
Public Member Functions inherited from DefaultParamHandler
| DefaultParamHandler (const String &name)
| Constructor with name that is displayed in error messages. More...
| DefaultParamHandler (const DefaultParamHandler &rhs)
| Copy constructor. More...
virtual | ~DefaultParamHandler ()
| Destructor. More...
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs)
| Assignment operator. More...
virtual bool | operator== (const DefaultParamHandler &rhs) const
| Equality operator. More...
void | setParameters (const Param &param)
| Sets the parameters. More...
const Param & | getParameters () const
| Non-mutable access to the parameters. More...
const Param & | getDefaults () const
| Non-mutable access to the default parameters. More...
const String & | getName () const
| Non-mutable access to the name. More...
void | setName (const String &name)
| Mutable access to the name. More...
const std::vector< String > & | getSubsections () const
| Non-mutable access to the registered subsections. More...

## 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...
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...
Reimplemented QT events
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
Protected Member Functions inherited from SpectrumCanvas
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...
LayerData & | getLayer_ (Size index)
| Returns the layer with index `index`. More...
LayerData & | getCurrentLayer_ ()
| Returns the currently active layer. More...
virtual void | changeVisibleArea_ (const AreaType &new_area, bool repaint=true, bool add_to_stack=false)
| Sets the visible area. 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 | 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 | 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...

## Protected Attributes

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...
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< LayerData > | layers_
| Layer data. More...
bool | mz_to_x_axis_
| Stores the mapping of m/z. More...
AreaType | visible_area_
| Stores the currently visible area. More...
DRange< 3 > | overall_data_range_
| Stores the data range (m/z, RT and intensity) of all layers. More...
bool | show_grid_
| Stores whether or not to show a grid. More...
std::vector< AreaType > | zoom_stack_
| The zoom stack. More...
std::vector< AreaType >::iterator | zoom_pos_
| The current position in the zoom stack. More...
bool | update_buffer_
| Whether to recalculate the data in the buffer when repainting. More...
Size | current_layer_
| Stores the index of the currently active layer. More...
SpectrumWidget * | spectrum_widget_
| Back-pointer to the enclosing spectrum widget. More...
QPoint | last_mouse_pos_
| start position of mouse actions More...
double | percentage_factor_
| Intensity scaling factor for relative scale with multiple layers. More...
std::vector< double > | snap_factors_
| Intensity scaling factor for 'snap to maximum intensity mode'. More...
QRubberBand | rubber_band_
| Rubber band for selected area. More...
QMenu * | context_add_
| External context menu extension. More...
bool | show_timing_
| Flag that determines if timing data is printed to the command line. More...
PeakIndex | selected_peak_
| selected peak More...
PeakIndex | measurement_start_
| start peak of measuring mode More...
Protected Attributes inherited from DefaultParamHandler
Param | param_
| Container for current parameters. More...
Param | defaults_
| Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String > | subsections_
| Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String | error_name_
| Name that is displayed in error messages during the parameter checking. More...
bool | check_defaults_
| If this member is set to false no checking if parameters in done;. More...
bool | warn_empty_defaults_
| If this member is set to false no warning is emitted when defaults are empty;. More...

## Private Member Functions

| 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...

## 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:

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)

## 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 | ) |

override slot

## ◆ 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_data2pixel | The current ratio of #data points vs. # pixels of image
  pen_size | In/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 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 | ) |

override protected

## ◆ currentLayerParametersChanged_

void currentLayerParametersChanged_ | ( |  | ) |

protected slot

Reacts on changed layer parameters.

## ◆ dataToWidget_()

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

inline protected

Convert chart to widget coordinates.

Translates chart coordinates to widget coordinates.

Parameters

  x | the chart coordinate x
  y | the chart coordinate y
  point | returned 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_ | ( |  | ) |

override protected virtual

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
| ) |  |

inline protected

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 | ) |

override slot

## ◆ intensityModeChange_()

void intensityModeChange_ | ( |  | ) |

override protected virtual

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_index | Index of the layer.
  ce | The ConsensusFeature that needs checking

## ◆ keyPressEvent()

void keyPressEvent | ( | QKeyEvent * | e | ) |

override protected

## ◆ keyReleaseEvent()

void keyReleaseEvent | ( | QKeyEvent * | e | ) |

override protected

## ◆ mergeIntoLayer() [1/3]

void mergeIntoLayer | ( | Size | i,
|  | FeatureMapSharedPtrType | map
| ) |  |

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

Referenced by TOPPViewBase::addData().

## ◆ mergeIntoLayer() [2/3]

void mergeIntoLayer | ( | Size | i,
|  | ConsensusMapSharedPtrType | map
| ) |  |

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

## ◆ 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 | ) |

override protected

## ◆ mouseMoveEvent()

void mouseMoveEvent | ( | QMouseEvent * | e | ) |

override protected

## ◆ mousePressEvent()

void mousePressEvent | ( | QMouseEvent * | e | ) |

override protected

## ◆ mouseReleaseEvent()

void mouseReleaseEvent | ( | QMouseEvent * | e | ) |

override protected

## ◆ 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_index | Index of the layer.
  cf | Reference to the feature to be painted.
  p | The QPainter to paint on.
  use_buffer | Flag 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_index | Index of the layer.
  p | The 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

  hulls | Reference to convex hull vector.
  p | The 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_index | The index of the layer.
  p | The QPainter to paint on.

## ◆ paintEvent()

void paintEvent | ( | QPaintEvent * | e | ) |

override protected

## ◆ paintFeatureConvexHulls_()

void paintFeatureConvexHulls_ | ( | Size | layer_index,
|  | QPainter & | p
| ) |  |

protected

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

Parameters

  layer_index | Index of the layer.
  p | The QPainter to paint on.

## ◆ paintFeatureData_()

void paintFeatureData_ | ( | Size | layer_index,
|  | QPainter & | p
| ) |  |

protected

Paints feature data.

Parameters

  layer_index | The index of the layer.
  p | The 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_index | Index of the layer.
  p | The 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_index | The index of the layer.
  rt_pixel_count |
  mz_pixel_count |
  p | The QPainter to paint on.

## ◆ paintPrecursorPeaks_()

void paintPrecursorPeaks_ | ( | Size | layer_index,
|  | QPainter & | painter
| ) |  |

protected

Paints the precursor peaks.

Parameters

  layer_index | The index of the layer.
  painter | The 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_index | Index of the layer.
  p | The QPainter to paint on.

## ◆ precalculatedColorIndex_()

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

inline protected

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_ | ( |  | ) |

override protected virtual

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

See also
  snap_factors_

Reimplemented from SpectrumCanvas.

## ◆ removeLayer

void removeLayer | ( | Size | layer_index | ) |

override slot

## ◆ saveCurrentLayer()

void saveCurrentLayer | ( | bool | visible | ) |

override virtual

Saves the current layer data.

Parameters

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

Implements SpectrumCanvas.

## ◆ showCurrentLayerPreferences()

void showCurrentLayerPreferences | ( |  | ) |

override virtual

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_ | ( |  | ) |

override protected virtual

Translation bound to the 'Down' key.

Reimplemented from SpectrumCanvas.

## ◆ translateForward_()

void translateForward_ | ( |  | ) |

override protected virtual

Translation bound to the 'Up' key.

Reimplemented from SpectrumCanvas.

## ◆ translateLeft_()

void translateLeft_ | ( | Qt::KeyboardModifiers | m | ) |

override protected virtual

Translation bound to the 'Left' key.

Reimplemented from SpectrumCanvas.

## ◆ translateRight_()

void translateRight_ | ( | Qt::KeyboardModifiers | m | ) |

override protected virtual

Translation bound to the 'Right' key.

Reimplemented from SpectrumCanvas.

## ◆ translateVisibleArea_()

virtual void translateVisibleArea_ | ( | double | mzShiftRel,
|  | double | rtShiftRel
| ) |  |

protected virtual

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

## ◆ updateLayer

void updateLayer | ( | Size | i | ) |

override slot

## ◆ 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_ | ( |  | ) |

override protected virtual

Updates the scroll bars.

Updates the scrollbars after a change of the visible area.

Reimplemented from SpectrumCanvas.

## ◆ verticalScrollBarChange

void verticalScrollBarChange | ( | int | value | ) |

override slot

## 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