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SpectrumCanvas.h
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34 
35 
36 #ifndef OPENMS_VISUAL_SPECTRUMCANVAS_H
37 #define OPENMS_VISUAL_SPECTRUMCANVAS_H
38 
39 //OpenMS
40 #include <OpenMS/CONCEPT/Types.h>
45 
46 //QT
47 #include <QtGui/QWidget>
48 #include <QtGui/QRubberBand>
49 class QWheelEvent;
50 class QKeyEvent;
51 class QMouseEvent;
52 class QFocusEvent;
53 class QMenu;
54 
55 //STL
56 #include <stack>
57 #include <vector>
58 
59 namespace OpenMS
60 {
61  class SpectrumWidget;
62 
94  class OPENMS_GUI_DLLAPI SpectrumCanvas :
95  public QWidget,
96  public DefaultParamHandler
97  {
98  Q_OBJECT
99 
100 public:
103 
116 
125 
130 
131 
134  {
137  AM_MEASURE
138  };
139 
142  {
146  IM_LOG
147  };
148 
150 
152  SpectrumCanvas(const Param & preferences, QWidget * parent = 0);
153 
155  virtual ~SpectrumCanvas();
156 
164  inline void setSpectrumWidget(SpectrumWidget * widget)
165  {
166  spectrum_widget_ = widget;
167  }
168 
176  {
177  return spectrum_widget_;
178  }
179 
186  inline Int getActionMode() const
187  {
188  return action_mode_;
189  }
190 
198  inline Int getIntensityMode() const
199  {
200  return intensity_mode_;
201  }
202 
213  {
214  intensity_mode_ = mod;
215  intensityModeChange_();
216  }
217 
223  inline bool gridLinesShown() const
224  {
225  return show_grid_;
226  }
227 
229  inline const LayerData & getLayer(Size index) const
230  {
231  OPENMS_PRECONDITION(index < layers_.size(), "SpectrumCanvas::getLayer(index) index overflow");
232  return layers_[index];
233  }
234 
236  inline const LayerData & getCurrentLayer() const
237  {
238  OPENMS_PRECONDITION(current_layer_ < layers_.size(), "SpectrumCanvas::getCurrentLayer() index overflow");
239  return layers_[current_layer_];
240  }
241 
243  inline Size getCurrentLayerIndex() const
244  {
245  return current_layer_;
246  }
247 
250  {
251  OPENMS_PRECONDITION(current_layer_ < layers_.size(), "SpectrumCanvas::getCurrentLayer() index overflow");
252  return layers_[current_layer_];
253  }
254 
257  {
258  return getLayerFlag(current_layer_, f);
259  }
260 
262  void setLayerFlag(LayerData::Flags f, bool value)
263  {
264  setLayerFlag(current_layer_, f, value);
265  }
266 
268  bool getLayerFlag(Size layer, LayerData::Flags f) const
269  {
270  OPENMS_PRECONDITION(layer < layers_.size(), "SpectrumCanvas::getLayerFlag() index overflow");
271  return layers_[layer].flags.test(f);
272  }
273 
275  void setLayerFlag(Size layer, LayerData::Flags f, bool value)
276  {
277  //abort if there are no layers
278  if (layers_.empty()) return;
279 
280  OPENMS_PRECONDITION(layer < layers_.size(), "SpectrumCanvas::setLayerFlag() index overflow");
281 
282  layers_[layer].flags.set(f, value);
283  update_buffer_ = true;
284  update();
285  }
286 
287  inline void setLabel(LayerData::LabelType label)
288  {
289  //abort if there are no layers
290  if (layers_.empty()) return;
291 
292  OPENMS_PRECONDITION(current_layer_ < layers_.size(), "SpectrumCanvas::setLabel() index overflow");
293  layers_[current_layer_].label = label;
294 
295  update_buffer_ = true;
296  update();
297  }
298 
304  inline const AreaType & getVisibleArea() const
305  {
306  return visible_area_;
307  }
308 
312  virtual void setFilters(const DataFilters & filters);
313 
315  inline bool isMzToXAxis()
316  {
317  return mz_to_x_axis_;
318  }
319 
321  void mzToXAxis(bool mz_to_x_axis);
322 
329  inline Size getLayerCount() const
331  {
332  return layers_.size();
333  }
334 
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 = "");
352 
361  bool addLayer(FeatureMapSharedPtrType map, const String & filename = "");
362 
371  bool addLayer(ConsensusMapSharedPtrType map, const String & filename = "");
373 
382  bool addLayer(std::vector<PeptideIdentification> & peptides,
383  const String & filename = "");
384 
387  {
388  if (getCurrentLayer().type == LayerData::DT_PEAK || getCurrentLayer().type == LayerData::DT_CHROMATOGRAM)
389  {
390  return getCurrentLayer().getPeakData()->getMinInt();
391  }
392  else if (getCurrentLayer().type == LayerData::DT_FEATURE)
393  {
394  return getCurrentLayer().getFeatureMap()->getMinInt();
395  }
396  else
397  {
398  return getCurrentLayer().getConsensusMap()->getMinInt();
399  }
400  }
401 
404  {
405  if (getCurrentLayer().type == LayerData::DT_PEAK || getCurrentLayer().type == LayerData::DT_CHROMATOGRAM)
406  {
407  return getCurrentLayer().getPeakData()->getMaxInt();
408  }
409  else if (getCurrentLayer().type == LayerData::DT_FEATURE)
410  {
411  return getCurrentLayer().getFeatureMap()->getMaxInt();
412  }
413  else
414  {
415  return getCurrentLayer().getConsensusMap()->getMaxInt();
416  }
417  }
418 
420  inline Real getMinIntensity(Size index) const
421  {
422  if (getLayer(index).type == LayerData::DT_PEAK || getCurrentLayer().type == LayerData::DT_CHROMATOGRAM)
423  {
424  return getLayer(index).getPeakData()->getMinInt();
425  }
426  else if (getLayer(index).type == LayerData::DT_FEATURE)
427  {
428  return getLayer(index).getFeatureMap()->getMinInt();
429  }
430  else
431  {
432  return getLayer(index).getConsensusMap()->getMinInt();
433  }
434  }
435 
437  inline Real getMaxIntensity(Size index) const
438  {
439  if (getLayer(index).type == LayerData::DT_PEAK || getCurrentLayer().type == LayerData::DT_CHROMATOGRAM)
440  {
441  return getLayer(index).getPeakData()->getMaxInt();
442  }
443  else if (getLayer(index).type == LayerData::DT_FEATURE)
444  {
445  return getLayer(index).getFeatureMap()->getMaxInt();
446  }
447  else
448  {
449  return getLayer(index).getConsensusMap()->getMaxInt();
450  }
451  }
452 
454  void setLayerName(Size i, const String & name);
455 
457  String getLayerName(Size i);
458 
460  inline void setCurrentLayerParameters(const Param & param)
461  {
462  getCurrentLayer_().param = param;
463  emit preferencesChange();
464  }
465 
471  const DRange<3> & getDataRange();
472 
478  DoubleReal getSnapFactor();
479 
481  DoubleReal getPercentageFactor();
482 
484  virtual void showCurrentLayerPreferences() = 0;
485 
492  virtual void showMetaData(bool modifiable = false, Int index = -1);
493 
499  virtual void saveCurrentLayer(bool visible) = 0;
500 
501 public slots:
502 
509  void changeVisibility(Size i, bool b);
510 
517  void changeLayerFilterState(Size i, bool b);
518 
525  void showGridLines(bool show);
526 
534  void resetZoom(bool repaint = true);
535 
542  void setVisibleArea(AreaType area);
543 
549  virtual void horizontalScrollBarChange(int value);
550 
556  virtual void verticalScrollBarChange(int value);
557 
559  void setAdditionalContextMenu(QMenu * menu);
560 
568  void getVisiblePeakData(ExperimentType & map) const;
569 
570 
578  void getVisibleFeatureData(FeatureMapType & map) const;
579 
587  void getVisibleConsensusData(ConsensusMapType & map) const;
588 
596  void getVisibleIdentifications(std::vector<PeptideIdentification> & peptides) const;
597 
599  virtual void updateLayer(Size i) = 0;
600 
601 signals:
602 
604  void layerModficationChange(Size layer, bool modified);
605 
607  void layerActivated(QWidget * w);
608 
610  void layerZoomChanged(QWidget * w);
611 
618  void visibleAreaChanged(DRange<2> area); //Do not change this to AreaType! QT needs the exact type...
619 
621  void sendCursorStatus(double mz = -1.0, double rt = -1.0);
622 
624  void sendStatusMessage(std::string message, OpenMS::UInt time);
625 
627  void recalculateAxes();
628 
630  void updateVScrollbar(float, float, float, float);
631 
633  void updateHScrollbar(float, float, float, float);
634 
636  void changeLegendVisibility();
637 
639  void actionModeChange();
640 
642  void preferencesChange();
643 
644 protected slots:
645 
647  void updateCursor_();
648 
649 protected:
650 
652  void drawText_(QPainter & painter, QStringList text);
653 
655  DoubleReal getIdentificationMZ_(const Size layer_index,
656  const PeptideIdentification & peptide) const;
657 
659  virtual bool finishAdding_() = 0;
660 
662  inline LayerData & getLayer_(Size index)
663  {
664  OPENMS_PRECONDITION(index < layers_.size(), "SpectrumCanvas::getLayer_(index) index overflow");
665  return layers_[index];
666  }
667 
670  {
671  return getLayer_(current_layer_);
672  }
673 
676  {
677  return getCurrentLayer_().getPeakData();
678  }
679 
681 
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);
690 
692  virtual void intensityModeChange_();
693 
704  virtual void changeVisibleArea_(const AreaType & new_area, bool repaint = true, bool add_to_stack = false);
705 
711  virtual void recalculateSnapFactor_();
712 
714 
715  virtual void zoom_(int x, int y, bool zoom_in);
718  void zoomBack_();
720  virtual void zoomForward_();
722  void zoomAdd_(const AreaType & area);
724  void zoomClear_();
726 
728 
729  virtual void translateLeft_();
732  virtual void translateRight_();
734  virtual void translateForward_();
736  virtual void translateBackward_();
738 
744  virtual void updateScrollbars_();
745 
746 
756  {
757  if (!isMzToXAxis())
758  {
759  return PointType(
760  visible_area_.minX() + (height() - y) / height() * visible_area_.width(),
761  visible_area_.minY() + x / width() * visible_area_.height()
762  );
763  }
764  else
765  {
766  return PointType(
767  visible_area_.minX() + x / width() * visible_area_.width(),
768  visible_area_.minY() + (height() - y) / height() * visible_area_.height()
769  );
770  }
771  }
772 
774  inline PointType widgetToData_(const QPoint & pos)
775  {
776  return widgetToData_(pos.x(), pos.y());
777  }
778 
787  inline void dataToWidget_(DoubleReal x, DoubleReal y, QPoint & point)
788  {
789  if (!isMzToXAxis())
790  {
791 
792 
793  if (intensity_mode_ != SpectrumCanvas::IM_LOG)
794  {
795  point.setX(int((y - visible_area_.minY()) / visible_area_.height() * width()));
796  }
797  else // IM_LOG
798  {
799  point.setX(int(
800  std::log10((y - visible_area_.minY()) + 1) / std::log10(visible_area_.height() + 1) * width())
801  );
802  }
803 
804  point.setY(height() - int((x - visible_area_.minX()) / visible_area_.width() * height()));
805  }
806  else
807  {
808  point.setX(int((x - visible_area_.minX()) / visible_area_.width() * width()));
809 
810  if (intensity_mode_ != SpectrumCanvas::IM_LOG)
811  {
812  point.setY(height() - int((y - visible_area_.minY()) / visible_area_.height() * height()));
813  }
814  else // IM_LOG
815  {
816  point.setY(height() - int(
817  std::log10((y - visible_area_.minY()) + 1) / std::log10(visible_area_.height() + 1) * height()
818  ));
819  }
820  }
821  }
822 
824  virtual void paintGridLines_(QPainter & painter);
825 
827  QImage buffer_;
828 
831 
834 
836  std::vector<LayerData> layers_;
837 
840 
848 
858  void recalculateRanges_(UInt mz_dim, UInt rt_dim, UInt it_dim);
859 
868 
871 
873  std::vector<AreaType> zoom_stack_;
875  std::vector<AreaType>::iterator zoom_pos_;
876 
886  virtual void update_(const char * caller_name);
887 
889  void modificationStatus_(Size layer_index, bool modified);
890 
893 
896 
898  void adjustBuffer_();
899 
902 
905 
912 
918  std::vector<DoubleReal> snap_factors_;
919 
921  QRubberBand rubber_band_;
922 
924  QMenu * context_add_;
925 
928 
933 
935  template <typename PeakType>
937  {
938  std::set<DataProcessing::ProcessingAction> actions;
939  actions.insert(action);
940 
941  DataProcessing p;
942  //actions
943  p.setProcessingActions(actions);
944  //software
945  p.getSoftware().setName("SpectrumCanvas");
946  //version
948  //time
950 
951  for (Size i = 0; i < map.size(); ++i)
952  {
953  map[i].getDataProcessing().push_back(p);
954  }
955  }
956 
957  };
958 }
959 
960 #endif
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 &#39;snap to maximum intensity mode&#39;.
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
Base class for spectrum widgets.
Definition: SpectrumWidget.h:71
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 &param)
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

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:21 using doxygen 1.8.5