SpectrumCanvas.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// 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);
      }
    }

  };
}