36 #ifndef OPENMS_VISUAL_SPECTRUMCANVAS_H
37 #define OPENMS_VISUAL_SPECTRUMCANVAS_H
47 #include <QtGui/QWidget>
48 #include <QtGui/QRubberBand>
166 spectrum_widget_ = widget;
177 return spectrum_widget_;
200 return intensity_mode_;
214 intensity_mode_ = mod;
215 intensityModeChange_();
231 OPENMS_PRECONDITION(index < layers_.size(),
"SpectrumCanvas::getLayer(index) index overflow");
232 return layers_[index];
238 OPENMS_PRECONDITION(current_layer_ < layers_.size(),
"SpectrumCanvas::getCurrentLayer() index overflow");
239 return layers_[current_layer_];
245 return current_layer_;
251 OPENMS_PRECONDITION(current_layer_ < layers_.size(),
"SpectrumCanvas::getCurrentLayer() index overflow");
252 return layers_[current_layer_];
258 return getLayerFlag(current_layer_, f);
264 setLayerFlag(current_layer_, f, value);
270 OPENMS_PRECONDITION(layer < layers_.size(),
"SpectrumCanvas::getLayerFlag() index overflow");
271 return layers_[layer].flags.test(f);
278 if (layers_.empty())
return;
280 OPENMS_PRECONDITION(layer < layers_.size(),
"SpectrumCanvas::setLayerFlag() index overflow");
282 layers_[layer].flags.set(f, value);
283 update_buffer_ =
true;
290 if (layers_.empty())
return;
292 OPENMS_PRECONDITION(current_layer_ < layers_.size(),
"SpectrumCanvas::setLabel() index overflow");
293 layers_[current_layer_].label = label;
295 update_buffer_ =
true;
306 return visible_area_;
312 virtual void setFilters(
const DataFilters & filters);
317 return mz_to_x_axis_;
321 void mzToXAxis(
bool mz_to_x_axis);
329 inline Size getLayerCount()
const
332 return layers_.size();
336 Size activeLayerIndex()
const;
338 virtual void activateLayer(
Size layer_index) = 0;
340 virtual void removeLayer(
Size layer_index) = 0;
351 bool addLayer(ExperimentSharedPtrType map,
const String & filename =
"");
361 bool addLayer(FeatureMapSharedPtrType map,
const String & filename =
"");
371 bool addLayer(ConsensusMapSharedPtrType map,
const String & filename =
"");
382 bool addLayer(std::vector<PeptideIdentification> & peptides,
383 const String & filename =
"");
390 return getCurrentLayer().getPeakData()->getMinInt();
394 return getCurrentLayer().getFeatureMap()->getMinInt();
398 return getCurrentLayer().getConsensusMap()->getMinInt();
407 return getCurrentLayer().getPeakData()->getMaxInt();
411 return getCurrentLayer().getFeatureMap()->getMaxInt();
415 return getCurrentLayer().getConsensusMap()->getMaxInt();
424 return getLayer(index).getPeakData()->getMinInt();
428 return getLayer(index).getFeatureMap()->getMinInt();
432 return getLayer(index).getConsensusMap()->getMinInt();
441 return getLayer(index).getPeakData()->getMaxInt();
445 return getLayer(index).getFeatureMap()->getMaxInt();
449 return getLayer(index).getConsensusMap()->getMaxInt();
454 void setLayerName(
Size i,
const String & name);
462 getCurrentLayer_().param = param;
463 emit preferencesChange();
484 virtual void showCurrentLayerPreferences() = 0;
492 virtual void showMetaData(
bool modifiable =
false,
Int index = -1);
499 virtual void saveCurrentLayer(
bool visible) = 0;
509 void changeVisibility(
Size i,
bool b);
517 void changeLayerFilterState(
Size i,
bool b);
525 void showGridLines(
bool show);
534 void resetZoom(
bool repaint =
true);
542 void setVisibleArea(AreaType area);
549 virtual void horizontalScrollBarChange(
int value);
556 virtual void verticalScrollBarChange(
int value);
559 void setAdditionalContextMenu(QMenu * menu);
568 void getVisiblePeakData(ExperimentType & map)
const;
578 void getVisibleFeatureData(FeatureMapType & map)
const;
587 void getVisibleConsensusData(ConsensusMapType & map)
const;
596 void getVisibleIdentifications(std::vector<PeptideIdentification> & peptides)
const;
599 virtual void updateLayer(
Size i) = 0;
604 void layerModficationChange(
Size layer,
bool modified);
607 void layerActivated(
QWidget * w);
610 void layerZoomChanged(
QWidget * w);
621 void sendCursorStatus(
double mz = -1.0,
double rt = -1.0);
624 void sendStatusMessage(std::string message,
OpenMS::UInt time);
627 void recalculateAxes();
630 void updateVScrollbar(
float,
float,
float,
float);
633 void updateHScrollbar(
float,
float,
float,
float);
636 void changeLegendVisibility();
639 void actionModeChange();
642 void preferencesChange();
647 void updateCursor_();
652 void drawText_(QPainter & painter, QStringList text);
659 virtual bool finishAdding_() = 0;
664 OPENMS_PRECONDITION(index < layers_.size(),
"SpectrumCanvas::getLayer_(index) index overflow");
665 return layers_[index];
671 return getLayer_(current_layer_);
677 return getCurrentLayer_().getPeakData();
682 void resizeEvent(QResizeEvent * e);
683 void wheelEvent(QWheelEvent * e);
684 void keyPressEvent(QKeyEvent * e);
685 void keyReleaseEvent(QKeyEvent * e);
686 void focusOutEvent(QFocusEvent * e);
687 void leaveEvent(QEvent * e);
688 void enterEvent(QEvent * e);
692 virtual void intensityModeChange_();
704 virtual void changeVisibleArea_(
const AreaType & new_area,
bool repaint =
true,
bool add_to_stack =
false);
711 virtual void recalculateSnapFactor_();
715 virtual void zoom_(
int x,
int y,
bool zoom_in);
720 virtual void zoomForward_();
722 void zoomAdd_(
const AreaType & area);
729 virtual void translateLeft_();
732 virtual void translateRight_();
734 virtual void translateForward_();
736 virtual void translateBackward_();
744 virtual void updateScrollbars_();
760 visible_area_.minX() + (height() - y) / height() * visible_area_.width(),
761 visible_area_.minY() + x / width() * visible_area_.height()
767 visible_area_.minX() + x / width() * visible_area_.width(),
768 visible_area_.minY() + (height() - y) / height() * visible_area_.height()
776 return widgetToData_(pos.x(), pos.y());
795 point.setX(
int((y - visible_area_.minY()) / visible_area_.height() * width()));
800 std::log10((y - visible_area_.minY()) + 1) / std::log10(visible_area_.height() + 1) * width())
804 point.setY(height() -
int((x - visible_area_.minX()) / visible_area_.width() * height()));
808 point.setX(
int((x - visible_area_.minX()) / visible_area_.width() * width()));
812 point.setY(height() -
int((y - visible_area_.minY()) / visible_area_.height() * height()));
816 point.setY(height() -
int(
817 std::log10((y - visible_area_.minY()) + 1) / std::log10(visible_area_.height() + 1) * height()
824 virtual void paintGridLines_(QPainter & painter);
858 void recalculateRanges_(
UInt mz_dim,
UInt rt_dim,
UInt it_dim);
886 virtual void update_(
const char * caller_name);
889 void modificationStatus_(
Size layer_index,
bool modified);
898 void adjustBuffer_();
935 template <
typename PeakType>
938 std::set<DataProcessing::ProcessingAction> actions;
939 actions.insert(action);
951 for (
Size i = 0; i < map.
size(); ++i)
953 map[i].getDataProcessing().push_back(p);
Flags
Flags that determine which information is shown.
Definition: LayerData.h:75
Descripton of the applied preprocessing steps.
Definition: DataProcessing.h:51
bool show_grid_
Stores whether or not to show a grid.
Definition: SpectrumCanvas.h:870
bool update_buffer_
Whether to recalculate the data in the buffer when repainting.
Definition: SpectrumCanvas.h:892
LayerData::ExperimentSharedPtrType ExperimentSharedPtrType
Main managed data type (experiment)
Definition: SpectrumCanvas.h:107
LayerData::FeatureMapType FeatureMapType
Main data type (features)
Definition: SpectrumCanvas.h:109
std::vector< DoubleReal > snap_factors_
Intensity scaling factor for 'snap to maximum intensity mode'.
Definition: SpectrumCanvas.h:918
Real getMaxIntensity(Size index) const
Returns the maximum intensity of the layer with index index.
Definition: SpectrumCanvas.h:437
std::vector< AreaType >::iterator zoom_pos_
The current position in the zoom stack.
Definition: SpectrumCanvas.h:875
float Real
Real type.
Definition: Types.h:109
Real getCurrentMaxIntensity() const
Returns the maximum intensity of the active layer.
Definition: SpectrumCanvas.h:403
SpectrumType::ConstIterator SpectrumConstIteratorType
Spectrum iterator type (iterates over peaks)
Definition: SpectrumCanvas.h:120
A more convenient string class.
Definition: String.h:56
bool getLayerFlag(Size layer, LayerData::Flags f) const
returns a layer flag of the layer layer
Definition: SpectrumCanvas.h:268
DPosition< 2 > PointType
Type of the Points.
Definition: SpectrumCanvas.h:127
Shows intensities normalized by layer maximum: f(x)=x/max(x)*100.
Definition: SpectrumCanvas.h:144
Size size() const
Definition: MSExperiment.h:117
bool show_timing_
Flag that determines if timimg data is printed to the command line.
Definition: SpectrumCanvas.h:927
const LayerData & getLayer(Size index) const
returns the layer data with index index
Definition: SpectrumCanvas.h:229
std::vector< LayerData > layers_
Layer data.
Definition: SpectrumCanvas.h:836
PointType widgetToData_(const QPoint &pos)
Calls widgetToData_ with x and y position of pos.
Definition: SpectrumCanvas.h:774
LayerData & getLayer_(Size index)
Returns the layer with index index.
Definition: SpectrumCanvas.h:662
LayerData::ConsensusMapType ConsensusMapType
Main data type (consensus features)
Definition: SpectrumCanvas.h:113
QImage buffer_
Buffer that stores the actual peak information.
Definition: SpectrumCanvas.h:827
A container for features.
Definition: FeatureMap.h:111
#define OPENMS_PRECONDITION(condition, message)
Precondition macro.
Definition: Macros.h:107
DRange< 3 > overall_data_range_
Stores the data range (m/z, RT and intensity) of all layers.
Definition: SpectrumCanvas.h:867
ActionModes
Mouse action modes.
Definition: SpectrumCanvas.h:133
LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType
Main managed data type (consensus features)
Definition: SpectrumCanvas.h:115
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:125
bool mz_to_x_axis_
Stores the mapping of m/z.
Definition: SpectrumCanvas.h:839
Base class for visualization canvas classes.
Definition: SpectrumCanvas.h:94
void setProcessingActions(const std::set< ProcessingAction > &actions)
sets the description of the applied processing
A container for consensus elements.
Definition: ConsensusMap.h:60
Int getIntensityMode() const
Returns the intensity mode.
Definition: SpectrumCanvas.h:198
Real getMinIntensity(Size index) const
Returns the minimum intensity of the layer with index index.
Definition: SpectrumCanvas.h:420
Size getCurrentLayerIndex() const
returns the index of the active layer
Definition: SpectrumCanvas.h:243
void setLabel(LayerData::LabelType label)
Definition: SpectrumCanvas.h:287
zoom
Definition: SpectrumCanvas.h:136
PointType widgetToData_(DoubleReal x, DoubleReal y)
Convert widget to chart coordinates.
Definition: SpectrumCanvas.h:755
SpectrumType::PeakType PeakType
Peak type.
Definition: SpectrumCanvas.h:122
void setSpectrumWidget(SpectrumWidget *widget)
Sets the spectrum widget.
Definition: SpectrumCanvas.h:164
boost::shared_ptr< ExperimentType > ExperimentSharedPtrType
SharedPtr on MSExperiment.
Definition: LayerData.h:120
Chromatogram data.
Definition: LayerData.h:69
PeakIndex selected_peak_
selected peak
Definition: SpectrumCanvas.h:930
void setLayerFlag(LayerData::Flags f, bool value)
sets a layer flag of the current layer
Definition: SpectrumCanvas.h:262
Shows the maximum displayed intensity as if it was the overall maximum intensity. ...
Definition: SpectrumCanvas.h:145
Size current_layer_
Stores the index of the currently active layer.
Definition: SpectrumCanvas.h:895
void setCompletionTime(const DateTime &completion_time)
sets the time of completition taking a DateTime object
ExperimentSharedPtrType currentPeakData_()
Returns the currently active layer (mutable)
Definition: SpectrumCanvas.h:675
const AreaType & getVisibleArea() const
Returns the currently visible area.
Definition: SpectrumCanvas.h:304
LayerData & getCurrentLayer_()
Returns the currently active layer.
Definition: SpectrumCanvas.h:669
PeakIndex measurement_start_
start peak of measuring mode
Definition: SpectrumCanvas.h:932
Feature data.
Definition: LayerData.h:67
bool gridLinesShown() const
Returns if the grid is currently shown.
Definition: SpectrumCanvas.h:223
void setIntensityMode(IntensityModes mod)
Sets the intensity mode.
Definition: SpectrumCanvas.h:212
ProcessingAction
Definition: DataProcessing.h:58
bool getLayerFlag(LayerData::Flags f) const
returns a layer flag of the current layer
Definition: SpectrumCanvas.h:256
SpectrumWidget * spectrum_widget_
Back-pointer to the enclosing spectrum widget.
Definition: SpectrumCanvas.h:901
Real getCurrentMinIntensity() const
Returns the minimum intensity of the active layer.
Definition: SpectrumCanvas.h:386
boost::shared_ptr< ConsensusMap > ConsensusMapSharedPtrType
SharedPtr on consensus features.
Definition: LayerData.h:114
bool isMzToXAxis()
Returns the mapping of m/z to axes.
Definition: SpectrumCanvas.h:315
LayerData & getCurrentLayer()
returns the layer data of the active layer
Definition: SpectrumCanvas.h:249
SpectrumWidget * getSpectrumWidget() const
Returns the spectrum widget.
Definition: SpectrumCanvas.h:175
const Software & getSoftware() const
returns a const reference to the software used for processing
void addDataProcessing_(MSExperiment< PeakType > &map, DataProcessing::ProcessingAction action) const
Data processing setter for peak maps.
Definition: SpectrumCanvas.h:936
boost::shared_ptr< FeatureMap<> > FeatureMapSharedPtrType
SharedPtr on feature map.
Definition: LayerData.h:108
void setVersion(const String &version)
sets the software version
Logarithmic mode.
Definition: SpectrumCanvas.h:146
PeakType PeakType
Peak type.
Definition: MSSpectrum.h:107
void setCurrentLayerParameters(const Param ¶m)
Sets the parameters of the current layer.
Definition: SpectrumCanvas.h:460
Management and storage of parameters / INI files.
Definition: Param.h:69
void setLayerFlag(Size layer, LayerData::Flags f, bool value)
sets a layer flag of the layer layer
Definition: SpectrumCanvas.h:275
Representation of a mass spectrometry experiment.
Definition: MSExperiment.h:68
QRubberBand rubber_band_
Rubber band for selected area.
Definition: SpectrumCanvas.h:921
double percentage_factor_
Intensity scaling factor for relative scale with multiple layers.
Definition: SpectrumCanvas.h:911
Normal mode: f(x)=x.
Definition: SpectrumCanvas.h:143
void dataToWidget_(DoubleReal x, DoubleReal y, QPoint &point)
Convert chart to widget coordinates.
Definition: SpectrumCanvas.h:787
static String getVersion()
Return the version number of OpenMS.
DRange< 2 > AreaType
Types of Ranges/Areas.
Definition: SpectrumCanvas.h:129
LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType
Main managed data type (features)
Definition: SpectrumCanvas.h:111
QMenu * context_add_
External context menu extension.
Definition: SpectrumCanvas.h:924
Int getActionMode() const
Returns the action mode.
Definition: SpectrumCanvas.h:186
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
FeatureMapType::FeatureType FeatureType
Feature type.
Definition: SpectrumCanvas.h:124
translate
Definition: SpectrumCanvas.h:135
LabelType
Label used in visualization.
Definition: LayerData.h:91
IntensityModes intensity_mode_
Stores the used intensity mode function.
Definition: SpectrumCanvas.h:833
Spectrum profile or centroided data.
Definition: LayerData.h:66
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:90
IntensityModes
Display modes of intensity.
Definition: SpectrumCanvas.h:141
static DateTime now()
Returns the current date and time.
DataFilter array providing some convenience functions.
Definition: DataFilters.h:53
void setName(const String &name)
sets the name of the software
LayerData::ExperimentType ExperimentType
Main data type (experiment)
Definition: SpectrumCanvas.h:105
ActionModes action_mode_
Stores the current action mode (Pick, Zoom, Translate)
Definition: SpectrumCanvas.h:830
AreaType visible_area_
Stores the currently visible area.
Definition: SpectrumCanvas.h:847
std::vector< AreaType > zoom_stack_
The zoom stack.
Definition: SpectrumCanvas.h:873
int Int
Signed integer type.
Definition: Types.h:100
Class that stores the data for one layer.
Definition: LayerData.h:58
Index of a peak or feature.
Definition: PeakIndex.h:51
QPoint last_mouse_pos_
start position of mouse actions
Definition: SpectrumCanvas.h:904
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
ExperimentType::SpectrumType SpectrumType
Spectrum type.
Definition: SpectrumCanvas.h:118
const LayerData & getCurrentLayer() const
returns the layer data of the active layer
Definition: SpectrumCanvas.h:236