Merge pull request OpenMS#5696 from cbielow/layer_refactor

Layer refactor #2

Author: cbielow

src/openms/include/OpenMS/MATH/MISC/MathFunctions.h

@@ -53,6 +53,32 @@ namespace OpenMS
   */
   namespace Math
   {
+
+    /**
+      @brief Given an interval/range and a new value, extend the range to include the new value if needed
+
+      @param min The current minimum of the range
+      @param max The current maximum of the range
+      @param value The new value which may extend the range
+      @return true if the range was modified
+    */
+    template<typename T>
+    bool extendRange(T& min, T& max, const T& value)
+    {
+      if (value < min)
+      {
+        min = value;
+        return true;
+      }
+      if (value > max)
+      {
+        max = value;
+        return true;
+      }
+      return false;
+    }
+
+
     /**
       @brief rounds @p x up to the next decimal power 10 ^ @p decPow
 

src/openms/include/OpenMS/MATH/STATISTICS/StatisticFunctions.h

@@ -37,18 +37,10 @@
 #include <OpenMS/CONCEPT/Exception.h>
 #include <OpenMS/CONCEPT/Types.h>
 
-// array_wrapper needs to be included before it is used
-// only in boost1.64+. See issue #2790
-#if OPENMS_BOOST_VERSION_MINOR >= 64
-#include <boost/serialization/array_wrapper.hpp>
-#endif
-#include <boost/function/function_base.hpp>
-#include <boost/lambda/casts.hpp>
-#include <boost/lambda/lambda.hpp>
-
+#include <algorithm>
+#include <cmath>
 #include <iterator>
 #include <numeric>
-#include <algorithm>
 
 namespace OpenMS
 {
@@ -511,7 +503,7 @@ namespace OpenMS
       /* assure both ranges have the same number of elements */
       checkIteratorsEqual(iter_b, end_b);
 
-      return (tp * tn - fp * fn) / sqrt((tp + fp) * (tp + fn) * (tn + fp) * (tn + fn));
+      return (tp * tn - fp * fn) / std::sqrt((tp + fp) * (tp + fn) * (tn + fp) * (tn + fn));
     }
 
     /**
@@ -555,7 +547,7 @@ namespace OpenMS
       }
       /* assure both ranges have the same number of elements */
       checkIteratorsEqual(iter_b, end_b);
-      return numerator / sqrt(denominator_a * denominator_b);
+      return numerator / std::sqrt(denominator_a * denominator_b);
     }
 
     /// Replaces the elements in vector @p w by their ranks
@@ -574,8 +566,7 @@ namespace OpenMS
       }
       //sort
       std::sort(w_idx.begin(), w_idx.end(),
-                boost::lambda::ret<bool>((&boost::lambda::_1->*& std::pair<Size, Value>::second) < 
-                                         (&boost::lambda::_2->*& std::pair<Size, Value>::second)));
+                [](const auto& pair1, const auto& pair2) { return pair1.second < pair2.second; });
       //replace pairs <orig_index, value> in w_idx by pairs <orig_index, rank>
       while (i < n)
       {
@@ -673,7 +664,7 @@ namespace OpenMS
         return 0;
       }
 
-      return sum_model_data / (sqrt(sqsum_data) * sqrt(sqsum_model));
+      return sum_model_data / (std::sqrt(sqsum_data) * std::sqrt(sqsum_model));
     }
 
     /// Helper class to gather (and dump) some statistics from a e.g. vector<double>.

src/openms/source/KERNEL/FeatureMap.cpp

@@ -263,7 +263,7 @@ namespace OpenMS
       DBoundingBox<2> box = this->operator[](i).getConvexHull().getBoundingBox();
       if (!box.isEmpty())
       {
-        //update RT
+        // update RT
         if (box.minPosition()[Peak2D::RT] < this->pos_range_.minPosition()[Peak2D::RT])
         {
           this->pos_range_.setMinX(box.minPosition()[Peak2D::RT]);

src/openms_gui/include/OpenMS/VISUAL/LayerDataBase.h

@@ -408,18 +408,15 @@ namespace OpenMS
     }
 
     /**
-    @brief Update ranges of all data structures
-
-    Updates ranges of all tracked data structures 
-    (spectra, chromatograms, features etc).
+      @brief Update ranges of the underlying data
     */
-    void updateRanges();
+    virtual void updateRanges() = 0;
 
     /// Returns the minimum intensity of the internal data, depending on type
-    float getMinIntensity() const;
+    virtual float getMinIntensity() const = 0;
 
     /// Returns the maximum intensity of the internal data, depending on type
-    float getMaxIntensity() const;
+    virtual float getMaxIntensity() const = 0;
 
     /// updates the PeakAnnotations in the current PeptideHit with manually changed annotations
     /// if no PeptideIdentification or PeptideHit for the spectrum exist, it is generated
@@ -485,7 +482,7 @@ namespace OpenMS
     /// get name augmented with attributes, e.g. [flipped], or '*' if modified
     String getDecoratedName() const;
 
-  private:
+  protected:
     /// Update current cached spectrum for easy retrieval
     void updateCache_();
 

src/openms_gui/include/OpenMS/VISUAL/LayerDataChrom.h

@@ -58,6 +58,25 @@ namespace OpenMS
     LayerDataChrom(LayerDataChrom&& ld) = default;
     /// move assignment
     LayerDataChrom& operator=(LayerDataChrom&& ld) = default;
+
+    void updateRanges() override
+    {
+      peak_map_->updateRanges();
+      // on_disc_peaks->updateRanges(); // note: this is not going to work since its on disk! We currently don't have a good way to access these ranges
+      chromatogram_map_->updateRanges();
+      cached_spectrum_.updateRanges();
+    }
+
+    float getMinIntensity() const override
+    {
+      return getPeakData()->getMinInt();
+    }
+
+    float getMaxIntensity() const override
+    {
+      return getPeakData()->getMaxInt();
+    }
+
   };
 
 } //namespace

src/openms_gui/include/OpenMS/VISUAL/LayerDataConsensus.h

@@ -58,6 +58,21 @@ namespace OpenMS
     LayerDataConsensus(LayerDataConsensus&& ld) = default;
     /// move assignment
     LayerDataConsensus& operator=(LayerDataConsensus&& ld) = default;
+
+    void updateRanges() override
+    {
+      consensus_map_->updateRanges();
+    }
+
+    float getMinIntensity() const override
+    {
+      return getConsensusMap()->getMinInt();
+    }
+
+    float getMaxIntensity() const override
+    {
+      return getConsensusMap()->getMaxInt();
+    }
   };
 
 }// namespace OpenMS

src/openms_gui/include/OpenMS/VISUAL/LayerDataFeature.h

@@ -60,21 +60,35 @@ namespace OpenMS
     /// move assignment
     LayerDataFeature& operator=(LayerDataFeature&& ld) = default;
 
+    void updateRanges() override
+    {
+      features_->updateRanges();
+    }
+
+    float getMinIntensity() const override
+    {
+      return getFeatureMap()->getMinInt();
+    }
+
+    float getMaxIntensity() const override
+    {
+      return getFeatureMap()->getMaxInt();
+    }
 
-    virtual const PepIds& getPeptideIds() const override
+    const PepIds& getPeptideIds() const override
     {
       return getFeatureMap()->getUnassignedPeptideIdentifications();
     }
-    virtual PepIds& getPeptideIds() override
+    PepIds& getPeptideIds() override
     {
       return getFeatureMap()->getUnassignedPeptideIdentifications();
     }
 
-    virtual void setPeptideIds(const PepIds& ids) override
+    void setPeptideIds(const PepIds& ids) override
     {
       getFeatureMap()->getUnassignedPeptideIdentifications() = ids;
     }
-    virtual void setPeptideIds(PepIds&& ids) override
+    void setPeptideIds(PepIds&& ids) override
     {
       getFeatureMap()->getUnassignedPeptideIdentifications() = std::move(ids);
     }

src/openms_gui/include/OpenMS/VISUAL/LayerDataIdent.h

@@ -60,7 +60,21 @@ namespace OpenMS
     /// move assignment
     LayerDataIdent& operator=(LayerDataIdent&& ld) = default;
 
-    
+    void updateRanges() override
+    {
+      // nothing to do...
+    }
+
+    float getMinIntensity() const override
+    {
+      return -1;
+    }
+
+    float getMaxIntensity() const override
+    {
+      return -1;
+    }
+
     virtual const PepIds& getPeptideIds() const override
     {
       return peptides_;

src/openms_gui/include/OpenMS/VISUAL/LayerDataPeak.h

@@ -58,6 +58,22 @@ namespace OpenMS
     LayerDataPeak(LayerDataPeak&& ld) = default;
     /// move assignment
     LayerDataPeak& operator=(LayerDataPeak&& ld) = default;
+    
+    void updateRanges() override
+    {
+      peak_map_->updateRanges();
+      // on_disc_peaks->updateRanges(); // note: this is not going to work since its on disk! We currently don't have a good way to access these ranges
+      cached_spectrum_.updateRanges();
+    }
+
+    float getMinIntensity() const override
+    {
+      return getPeakData()->getMinInt();
+    }
+    float getMaxIntensity() const override
+    {
+      return getPeakData()->getMaxInt();
+    }
   };
 
 }// namespace OpenMS

src/openms_gui/include/OpenMS/VISUAL/PlotCanvas.h

@@ -843,24 +843,24 @@ protected slots:
     QImage buffer_;
 
     /// Stores the current action mode (Pick, Zoom, Translate)
-    ActionModes action_mode_;
+    ActionModes action_mode_ = AM_TRANSLATE;
 
     /// Stores the used intensity mode function
-    IntensityModes intensity_mode_;
+    IntensityModes intensity_mode_ = IM_NONE;
 
     /// Layer data
     LayerStack layers_;
 
     /// Stores the mapping of m/z
-    bool mz_to_x_axis_;
+    bool mz_to_x_axis_ = true;
 
     /**
         @brief Stores the currently visible area.
 
         Dimension 0 is the m/z dimension.@n
         Dimension 1 is the RT dimension (2D and 3D view) or the intensity dimension (1D view).
     */
-    AreaType visible_area_;
+    AreaType visible_area_ = AreaType::empty;
 
     /**
         @brief Recalculates the overall_data_range_
@@ -880,15 +880,15 @@ protected slots:
         Dimension 1 is the RT dimension (2D and 3D view) or the intensity dimension (1D view).@n
         Dimension 2 is the intensity dimension (2D and 3D view) or the RT dimension (1D view).
     */
-    DRange<3> overall_data_range_;
+    DRange<3> overall_data_range_ = DRange<3>::empty;
 
     /// Stores whether or not to show a grid.
-    bool show_grid_;
+    bool show_grid_ = true;
 
     /// The zoom stack.
     std::vector<AreaType> zoom_stack_;
     /// The current position in the zoom stack
-    std::vector<AreaType>::iterator zoom_pos_;
+    std::vector<AreaType>::iterator zoom_pos_ = zoom_stack_.end();
 
     /**
         @brief Updates the displayed data
@@ -905,10 +905,10 @@ protected slots:
     void modificationStatus_(Size layer_index, bool modified);
 
     /// Whether to recalculate the data in the buffer when repainting
-    bool update_buffer_;
+    bool update_buffer_ = false;
 
     /// Back-pointer to the enclosing spectrum widget
-    PlotWidget * spectrum_widget_;
+    PlotWidget* spectrum_widget_ = nullptr;
 
     /// start position of mouse actions
     QPoint last_mouse_pos_;
@@ -918,7 +918,7 @@ protected slots:
 
         In this mode all layers are scaled to the same maximum.
     */
-    double percentage_factor_;
+    double percentage_factor_ = 1.0;
 
     /**
         @brief Intensity scaling factor for 'snap to maximum intensity mode'.
@@ -927,16 +927,16 @@ protected slots:
 
         One entry per layer.
     */
-    std::vector<double> snap_factors_;
+    std::vector<double> snap_factors_ = {1.0};
 
     /// Rubber band for selected area
     QRubberBand rubber_band_;
 
     /// External context menu extension
-    QMenu* context_add_;
+    QMenu* context_add_ = nullptr;
 
     /// Flag that determines if timing data is printed to the command line
-    bool show_timing_;
+    bool show_timing_ = false;
 
     /// selected peak
     PeakIndex selected_peak_;