SpectrumCanvas.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
 
#pragma once
 
// OpenMS_GUI config
#include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
 
//OpenMS
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/VersionInfo.h>
#include <OpenMS/DATASTRUCTURES/DRange.h>
#include <OpenMS/VISUAL/LayerData.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 
//QT
#include <QtWidgets>
#include <QRubberBand>
 
class QWheelEvent;
class QKeyEvent;
class QMouseEvent;
class QFocusEvent;
class QMenu;
 
//STL
#include <stack>
#include <vector>
 
namespace OpenMS
{
  class SpectrumWidget;
 
  class OPENMS_GUI_DLLAPI SpectrumCanvas :
    public QWidget,
    public DefaultParamHandler
  {
    Q_OBJECT
 
public:
 
    typedef LayerData::ExperimentType ExperimentType;
    typedef LayerData::ExperimentSharedPtrType ExperimentSharedPtrType;
    typedef LayerData::ConstExperimentSharedPtrType ConstExperimentSharedPtrType;
    typedef LayerData::ODExperimentSharedPtrType ODExperimentSharedPtrType;
    typedef LayerData::FeatureMapType FeatureMapType;
    typedef LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType;
    typedef LayerData::ConsensusMapType ConsensusMapType;
    typedef LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType;
 
    typedef ExperimentType::SpectrumType SpectrumType;
    typedef SpectrumType::ConstIterator SpectrumConstIteratorType;
    typedef SpectrumType::PeakType PeakType;
    typedef FeatureMapType::FeatureType FeatureType;
 
    typedef DPosition<2> PointType;
    typedef DRange<2> AreaType;
 
 
    enum ActionModes
    {
      AM_TRANSLATE,   
      AM_ZOOM,        
      AM_MEASURE      
    };
 
    enum IntensityModes
    {
      IM_NONE,        
      IM_PERCENTAGE,  
      IM_SNAP,        
      IM_LOG          
    };
 
 
    SpectrumCanvas(const Param & preferences, QWidget * parent = nullptr);
 
    ~SpectrumCanvas() override;
 
    inline void setSpectrumWidget(SpectrumWidget * widget)
    {
      spectrum_widget_ = widget;
    }
 
    inline SpectrumWidget * getSpectrumWidget() const
    {
      return spectrum_widget_;
    }
 
    inline Int getActionMode() const
    {
      return action_mode_;
    }
 
    inline IntensityModes getIntensityMode() const
    {
      return intensity_mode_;
    }
 
    inline void setIntensityMode(IntensityModes mod)
    {
      intensity_mode_ = mod;
      intensityModeChange_();
    }
 
    inline bool gridLinesShown() const
    {
      return show_grid_;
    }
 
    inline const LayerData & getLayer(Size index) const
    {
      OPENMS_PRECONDITION(index < layers_.size(), "SpectrumCanvas::getLayer(index) index overflow");
      return layers_[index];
    }
 
    inline const LayerData & getCurrentLayer() const
    {
      OPENMS_PRECONDITION(current_layer_ < layers_.size(), "SpectrumCanvas::getCurrentLayer() index overflow");
      return layers_[current_layer_];
    }
 
    inline Size getCurrentLayerIndex() const
    {
      return current_layer_;
    }
 
    inline LayerData & getCurrentLayer()
    {
      OPENMS_PRECONDITION(current_layer_ < layers_.size(), "SpectrumCanvas::getCurrentLayer() index overflow");
      return layers_[current_layer_];
    }
 
    bool getLayerFlag(LayerData::Flags f) const
    {
      return getLayerFlag(current_layer_, f);
    }
 
    void setLayerFlag(LayerData::Flags f, bool value)
    {
      setLayerFlag(current_layer_, f, value);
    }
 
    bool getLayerFlag(Size layer, LayerData::Flags f) const
    {
      OPENMS_PRECONDITION(layer < layers_.size(), "SpectrumCanvas::getLayerFlag() index overflow");
      return layers_[layer].flags.test(f);
    }
 
    void setLayerFlag(Size layer, LayerData::Flags f, bool value)
    {
      //abort if there are no layers
      if (layers_.empty()) return;
 
      OPENMS_PRECONDITION(layer < layers_.size(), "SpectrumCanvas::setLayerFlag() index overflow");
 
      layers_[layer].flags.set(f, value);
      update_buffer_ = true;
      update();
    }
 
    inline void setLabel(LayerData::LabelType label)
    {
      //abort if there are no layers
      if (layers_.empty()) return;
 
      OPENMS_PRECONDITION(current_layer_ < layers_.size(), "SpectrumCanvas::setLabel() index overflow");
      layers_[current_layer_].label = label;
 
      update_buffer_ = true;
      update();
    }
 
    inline const AreaType & getVisibleArea() const
    {
      return visible_area_;
    }
 
    virtual void setFilters(const DataFilters & filters);
 
    inline bool isMzToXAxis()
    {
      return mz_to_x_axis_;
    }
 
    void mzToXAxis(bool mz_to_x_axis);
 
    inline Size getLayerCount() const
    {
      return layers_.size();
    }
 
    Size activeLayerIndex() const;
    virtual void activateLayer(Size layer_index) = 0;
    virtual void removeLayer(Size layer_index) = 0;
 
    bool addLayer(ExperimentSharedPtrType map, ODExperimentSharedPtrType od_map, const String & filename = "");
 
    bool addLayer(FeatureMapSharedPtrType map, const String & filename = "");
 
    bool addLayer(ConsensusMapSharedPtrType map, const String & filename = "");
 
    bool addLayer(std::vector<PeptideIdentification> & peptides,
                  const String & filename = "");
 
    inline float getCurrentMinIntensity() const
    {
      if (getCurrentLayer().type == LayerData::DT_PEAK || getCurrentLayer().type == LayerData::DT_CHROMATOGRAM)
      {
        return getCurrentLayer().getPeakData()->getMinInt();
      }
      else if (getCurrentLayer().type == LayerData::DT_FEATURE)
      {
        return getCurrentLayer().getFeatureMap()->getMinInt();
      }
      else
      {
        return getCurrentLayer().getConsensusMap()->getMinInt();
      }
    }
 
    inline float getCurrentMaxIntensity() const
    {
      if (getCurrentLayer().type == LayerData::DT_PEAK || getCurrentLayer().type == LayerData::DT_CHROMATOGRAM)
      {
        return getCurrentLayer().getPeakData()->getMaxInt();
      }
      else if (getCurrentLayer().type == LayerData::DT_FEATURE)
      {
        return getCurrentLayer().getFeatureMap()->getMaxInt();
      }
      else
      {
        return getCurrentLayer().getConsensusMap()->getMaxInt();
      }
    }
 
    inline float getMinIntensity(Size index) const
    {
      if (getLayer(index).type == LayerData::DT_PEAK || getCurrentLayer().type == LayerData::DT_CHROMATOGRAM)
      {
        return getLayer(index).getPeakData()->getMinInt();
      }
      else if (getLayer(index).type == LayerData::DT_FEATURE)
      {
        return getLayer(index).getFeatureMap()->getMinInt();
      }
      else
      {
        return getLayer(index).getConsensusMap()->getMinInt();
      }
    }
 
    inline float getMaxIntensity(Size index) const
    {
      if (getLayer(index).type == LayerData::DT_PEAK || getCurrentLayer().type == LayerData::DT_CHROMATOGRAM)
      {
        return getLayer(index).getPeakData()->getMaxInt();
      }
      else if (getLayer(index).type == LayerData::DT_FEATURE)
      {
        return getLayer(index).getFeatureMap()->getMaxInt();
      }
      else
      {
        return getLayer(index).getConsensusMap()->getMaxInt();
      }
    }
 
    void setLayerName(Size i, const String & name);
 
    String getLayerName(Size i);
 
    inline void setCurrentLayerParameters(const Param & param)
    {
      getCurrentLayer_().param = param;
      emit preferencesChange();
    }
 
    const DRange<3> & getDataRange();
 
    double getSnapFactor();
 
    double getPercentageFactor();
 
    virtual void showCurrentLayerPreferences() = 0;
 
    virtual void showMetaData(bool modifiable = false, Int index = -1);
 
    virtual void saveCurrentLayer(bool visible) = 0;
 
public slots:
 
    void changeVisibility(Size i, bool b);
 
    void changeLayerFilterState(Size i, bool b);
 
    void showGridLines(bool show);
 
    void resetZoom(bool repaint = true);
 
    void setVisibleArea(AreaType area);
 
    virtual void horizontalScrollBarChange(int value);
 
    virtual void verticalScrollBarChange(int value);
 
    void setAdditionalContextMenu(QMenu * menu);
 
    void getVisiblePeakData(ExperimentType & map) const;
 
 
    void getVisibleFeatureData(FeatureMapType & map) const;
 
    void getVisibleConsensusData(ConsensusMapType & map) const;
 
    void getVisibleIdentifications(std::vector<PeptideIdentification> & peptides) const;
 
    virtual void updateLayer(Size i) = 0;
 
signals:
 
    void layerModficationChange(Size layer, bool modified);
 
    void layerActivated(QWidget * w);
 
    void layerZoomChanged(QWidget * w);
 
    void visibleAreaChanged(DRange<2> area);     //Do not change this to AreaType! QT needs the exact type...
 
    void sendCursorStatus(double mz = -1.0, double rt = -1.0);
 
    void sendStatusMessage(std::string message, OpenMS::UInt time);
 
    void recalculateAxes();
 
    void updateVScrollbar(float, float, float, float);
 
    void updateHScrollbar(float, float, float, float);
 
    void changeLegendVisibility();
 
    void actionModeChange();
 
    void preferencesChange();
 
protected slots:
 
    void updateCursor_();
 
protected:
 
    void drawText_(QPainter & painter, QStringList text);
 
    double getIdentificationMZ_(const Size layer_index,
                                    const PeptideIdentification & peptide) const;
 
    virtual bool finishAdding_() = 0;
 
    inline LayerData & getLayer_(Size index)
    {
      OPENMS_PRECONDITION(index < layers_.size(), "SpectrumCanvas::getLayer_(index) index overflow");
      return layers_[index];
    }
 
    inline LayerData & getCurrentLayer_()
    {
      return getLayer_(current_layer_);
    }
 
 
    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 intensityModeChange_();
 
    virtual void changeVisibleArea_(const AreaType & new_area, bool repaint = true, bool add_to_stack = false);
 
    virtual void recalculateSnapFactor_();
 
 
    virtual void zoom_(int x, int y, bool zoom_in);
    void zoomBack_();
    virtual void zoomForward_();
    void zoomAdd_(const AreaType & area);
    void zoomClear_();
 
 
    virtual void translateLeft_(Qt::KeyboardModifiers m);
    virtual void translateRight_(Qt::KeyboardModifiers m);
    virtual void translateForward_();
    virtual void translateBackward_();
 
    virtual void updateScrollbars_();
 
    inline PointType widgetToData_(double x, double y)
    {
      if (!isMzToXAxis())
      {
        return PointType(
                 visible_area_.minX() + (height() - y) / height()  * visible_area_.width(),
                 visible_area_.minY() + x  / width() * visible_area_.height()
                 );
      }
      else
      {
        return PointType(
                 visible_area_.minX() + x / width() * visible_area_.width(),
                 visible_area_.minY() + (height() - y) / height() * visible_area_.height()
                 );
      }
    }
 
    inline PointType widgetToData_(const QPoint & pos)
    {
      return widgetToData_(pos.x(), pos.y());
    }
 
    inline void dataToWidget_(double x, double y, QPoint & point)
    {
      if (!isMzToXAxis())
      {
 
 
        if (intensity_mode_ != SpectrumCanvas::IM_LOG)
        {
          point.setX(int((y - visible_area_.minY()) / visible_area_.height() * width()));
        }
        else    // IM_LOG
        {
          point.setX(int(
                       std::log10((y - visible_area_.minY()) + 1) / std::log10(visible_area_.height() + 1) * width())
                     );
        }
 
        point.setY(height() - int((x - visible_area_.minX()) / visible_area_.width() * height()));
      }
      else
      {
        point.setX(int((x - visible_area_.minX()) / visible_area_.width() * width()));
 
        if (intensity_mode_ != SpectrumCanvas::IM_LOG)
        {
          point.setY(height() - int((y - visible_area_.minY()) / visible_area_.height() * height()));
        }
        else    // IM_LOG
        {
          point.setY(height() - int(
                       std::log10((y - visible_area_.minY()) + 1) / std::log10(visible_area_.height() + 1) * height()
                       ));
        }
      }
    }
 
    virtual void paintGridLines_(QPainter & painter);
 
    QImage buffer_;
 
    ActionModes action_mode_;
 
    IntensityModes intensity_mode_;
 
    std::vector<LayerData> layers_;
 
    bool mz_to_x_axis_;
 
    AreaType visible_area_;
 
    void recalculateRanges_(UInt mz_dim, UInt rt_dim, UInt it_dim);
 
    DRange<3> overall_data_range_;
 
    bool show_grid_;
 
    std::vector<AreaType> zoom_stack_;
    std::vector<AreaType>::iterator zoom_pos_;
 
    virtual void update_(const char * caller_name);
 
    void modificationStatus_(Size layer_index, bool modified);
 
    bool update_buffer_;
 
    Size current_layer_;
 
    void adjustBuffer_();
 
    SpectrumWidget * spectrum_widget_;
 
    QPoint last_mouse_pos_;
 
    double percentage_factor_;
 
    std::vector<double> snap_factors_;
 
    QRubberBand rubber_band_;
 
    QMenu * context_add_;
 
    bool show_timing_;
 
    PeakIndex selected_peak_;
    PeakIndex measurement_start_;
 
    void addDataProcessing_(PeakMap & map, DataProcessing::ProcessingAction action) const
    {
      std::set<DataProcessing::ProcessingAction> actions;
      actions.insert(action);
 
      DataProcessingPtr p = boost::shared_ptr<DataProcessing>(new DataProcessing);
      //actions
      p->setProcessingActions(actions);
      //software
      p->getSoftware().setName("SpectrumCanvas");
      //version
      p->getSoftware().setVersion(VersionInfo::getVersion());
      //time
      p->setCompletionTime(DateTime::now());
 
      for (Size i = 0; i < map.size(); ++i)
      {
        map[i].getDataProcessing().push_back(p);
      }
    }
 
  };
}