A Painter1D class for Peaks

doc/code_examples/Tutorial_GUI_Plot1D.cpp

@@ -28,32 +28,36 @@
 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 
-#include <QApplication>
-#include <OpenMS/VISUAL/Plot1DWidget.h>
 #include <OpenMS/FORMAT/DTAFile.h>
-#include <OpenMS/KERNEL/StandardTypes.h>
 #include <OpenMS/KERNEL/OnDiscMSExperiment.h>
+#include <OpenMS/KERNEL/StandardTypes.h>
 #include <OpenMS/VISUAL/LayerDataBase.h>
+#include <OpenMS/VISUAL/Plot1DWidget.h>
+#include <OpenMS/VISUAL/Plot2DWidget.h>
+#include <OpenMS/openms_data_path.h>
+#include <QApplication>
 
 using namespace OpenMS;
 using namespace std;
 
-Int main(int argc, const char ** argv)
+Int main(int argc, const char** argv)
 {
-  if (argc < 2) return 1;
-  // the path to the data should be given on the command line
-  String tutorial_data_path(argv[1]);
-
-  QApplication app(argc, const_cast<char **>(argv));
+  String tutorial_data_path(OPENMS_DOC_PATH + String("/code_examples/data/Tutorial_Spectrum1D.dta"));
+  if (argc >= 2)
+  { // the path to the data can be given on the command line
+    tutorial_data_path = argv[1];
+  }
+
+  QApplication app(argc, const_cast<char**>(argv));
 
   PeakMap exp;
   exp.resize(1);
-  DTAFile().load(tutorial_data_path + "/data/Tutorial_Spectrum1D.dta", exp[0]);
+  DTAFile().load(tutorial_data_path, exp[0]);
   LayerDataBase::ExperimentSharedPtrType exp_sptr(new PeakMap(exp));
   LayerDataBase::ODExperimentSharedPtrType on_disc_exp_sptr(new OnDiscMSExperiment());
-  Plot1DWidget * widget = new Plot1DWidget(Param(), nullptr);
+  auto* widget = new Plot1DWidget(Param(), nullptr);
   widget->canvas()->addLayer(exp_sptr, on_disc_exp_sptr);
   widget->show();
 
   return app.exec();
-} //end of main
+} // end of main

src/openms/include/OpenMS/FORMAT/HANDLERS/XMLHandler.h

@@ -40,21 +40,20 @@
 #include <OpenMS/DATASTRUCTURES/ListUtils.h> // StringList
 #include <OpenMS/DATASTRUCTURES/DateTime.h>
 #include <OpenMS/DATASTRUCTURES/ListUtils.h>
-#include <OpenMS/METADATA/MetaInfoInterface.h>
 
 #include <xercesc/util/XMLString.hpp>
 #include <xercesc/sax2/DefaultHandler.hpp>
-#include <xercesc/sax/Locator.hpp>
 #include <xercesc/sax2/Attributes.hpp>
 
 #include <iosfwd>
 #include <string>
 #include <memory>
 
+
 namespace OpenMS
 {
   class ProteinIdentification;
-
+  class MetaInfoInterface;
 
   namespace Internal
   {

src/openms/source/FORMAT/CVMappingFile.cpp

@@ -35,6 +35,7 @@
 #include <OpenMS/FORMAT/CVMappingFile.h>
 #include <OpenMS/DATASTRUCTURES/CVReference.h>
 #include <OpenMS/DATASTRUCTURES/CVMappingTerm.h>
+#include <OpenMS/DATASTRUCTURES/DataValue.h>
 #include <OpenMS/SYSTEM/File.h>
 
 using namespace xercesc;

src/openms/source/FORMAT/ControlledVocabulary.cpp

@@ -34,8 +34,9 @@
 
 #include <OpenMS/FORMAT/ControlledVocabulary.h>
 
-#include <OpenMS/SYSTEM/File.h>
+#include <OpenMS/DATASTRUCTURES/DataValue.h>
 #include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
+#include <OpenMS/SYSTEM/File.h>
 
 #include <iostream>
 #include <fstream>

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

@@ -49,6 +49,7 @@
 #include <OpenMS/METADATA/PeptideIdentification.h>
 #include <OpenMS/METADATA/ProteinIdentification.h>
 #include <OpenMS/VISUAL/ANNOTATION/Annotations1DContainer.h>
+//#include <OpenMS/VISUAL/Painter1DBase.h>
 #include <OpenMS/VISUAL/LogWindow.h>
 #include <OpenMS/VISUAL/MultiGradient.h>
 
@@ -64,6 +65,7 @@ namespace OpenMS
   class LayerStatistics;
   class OnDiscMSExperiment;
   class OSWData;
+  class Painter1DBase;
 
   /**
   @brief Class that stores the data for one layer
@@ -171,19 +173,21 @@ namespace OpenMS
 
     /// Default constructor
     LayerDataBase() = delete;
-    /// Ctor for child classes
+    /// C'tor for child classes
     LayerDataBase(const DataType type) : type(type) {};
     /// no Copy-ctor (should not be needed)
     LayerDataBase(const LayerDataBase& ld) = delete;
     /// no assignment operator (should not be needed)
     LayerDataBase& operator=(const LayerDataBase& ld) = delete;
-    /// move Ctor
+    /// move C'tor
     LayerDataBase(LayerDataBase&& ld) = default;
     /// move assignment
     LayerDataBase& operator=(LayerDataBase&& ld) = default;
-    /// Dtor
+    /// D'tor
     virtual ~LayerDataBase() = default;
 
+    virtual std::unique_ptr<Painter1DBase> getPainter1D() const = 0;
+
 
     /// Returns a const reference to the current feature data
     const FeatureMapSharedPtrType& getFeatureMap() const
@@ -267,11 +271,11 @@ namespace OpenMS
       return chromatogram_map_;
     }
 
-    /// get annotation (e.g. to build a hierachical ID View)
+    /// get annotation (e.g. to build a hierarchical ID View)
     /// Not const, because we might have incomplete data, which needs to be loaded from sql source
     OSWDataSharedPtrType& getChromatogramAnnotation();
 
-    /// get annotation (e.g. to build a hierachical ID View)
+    /// get annotation (e.g. to build a hierarchical ID View)
     /// Not actually const (only the pointer, not the data), because we might have incomplete data, which needs to be loaded from sql source
     const OSWDataSharedPtrType& getChromatogramAnnotation() const;
 

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

@@ -54,11 +54,13 @@ namespace OpenMS
     LayerDataChrom(const LayerDataChrom& ld) = delete;
     /// no assignment operator (should not be needed)
     LayerDataChrom& operator=(const LayerDataChrom& ld) = delete;
-    /// move Ctor
+    /// move C'tor
     LayerDataChrom(LayerDataChrom&& ld) = default;
     /// move assignment
     LayerDataChrom& operator=(LayerDataChrom&& ld) = default;
 
+    std::unique_ptr<Painter1DBase> getPainter1D() const override;
+
     void updateRanges() override
     {
       peak_map_->updateRanges();

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

@@ -58,6 +58,8 @@ namespace OpenMS
     /// move assignment
     LayerDataConsensus& operator=(LayerDataConsensus&& ld) = default;
 
+    std::unique_ptr<Painter1DBase> getPainter1D() const override;
+
     void updateRanges() override
     {
       consensus_map_->updateRanges();

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

@@ -54,11 +54,13 @@ namespace OpenMS
     LayerDataFeature(const LayerDataFeature& ld) = delete;
     /// no assignment operator (should not be needed)
     LayerDataFeature& operator=(const LayerDataFeature& ld) = delete;
-    /// move Ctor
+    /// move C'tor
     LayerDataFeature(LayerDataFeature&& ld) = default;
     /// move assignment
     LayerDataFeature& operator=(LayerDataFeature&& ld) = default;
 
+    std::unique_ptr<Painter1DBase> getPainter1D() const override;
+
     void updateRanges() override
     {
       features_->updateRanges();

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

@@ -60,6 +60,8 @@ namespace OpenMS
     /// move assignment
     LayerDataIdent& operator=(LayerDataIdent&& ld) = default;
 
+    std::unique_ptr<Painter1DBase> getPainter1D() const override;
+
     void updateRanges() override
     {
       // nothing to do...

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

@@ -58,6 +58,8 @@ namespace OpenMS
     /// move assignment
     LayerDataPeak& operator=(LayerDataPeak&& ld) = default;
 
+    std::unique_ptr<Painter1DBase> getPainter1D() const override;
+
     void updateRanges() override
     {
       peak_map_->updateRanges();

src/openms_gui/include/OpenMS/VISUAL/Painter1DBase.h

@@ -0,0 +1,88 @@
+// --------------------------------------------------------------------------
+//                   OpenMS -- Open-Source Mass Spectrometry
+// --------------------------------------------------------------------------
+// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
+// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
+//
+// 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: Chris Bielow $
+// $Authors: Chris Bielow $
+// --------------------------------------------------------------------------
+
+#pragma once
+
+#include <OpenMS/VISUAL/LayerDataBase.h>
+
+class QPainter;
+class QPenStyle;
+
+namespace OpenMS
+{
+  class LayerDataPeak;
+  class Plot1DCanvas;
+
+  /**
+   * @brief A base class for painting all items from a data layer (as supported by class derived from here) onto a 1D Canvas
+  */
+  class OPENMS_GUI_DLLAPI Painter1DBase
+  {
+  public:
+    /**
+       @brief Paints items using the given painter onto the canvas.
+
+       @param painter The painter used for drawing 
+       @param canvas The canvas to paint onto (should expose all the details needed, like canvas size, draw mode, colors etc)
+       @param layer_index Which layer is currently painted (FIXME: remove when Canvas1D::DrawMode and PenStyle are factored out) 
+    */
+    virtual void paint(QPainter*, Plot1DCanvas* canvas, int layer_index) = 0;
+
+    /// static method to draw a dashed line
+    static void drawDashedLine(const QPoint& from, const QPoint& to, QPainter* painter, QColor color);
+  };
+
+  /**
+     @brief Painter1D for spectra
+
+  */
+  class OPENMS_GUI_DLLAPI Painter1DPeak : public Painter1DBase
+  {
+  public:
+    /// C'tor which remembers the layer to paint
+    Painter1DPeak(const LayerDataPeak* parent);
+
+    /// Implementation of base class
+    void paint(QPainter*, Plot1DCanvas* canvas, int layer_index) override;
+
+  protected:
+    /// draw all Annotation1DItems attached to the layer
+    void drawAnnotations_(QPainter& painter, Plot1DCanvas* canvas);
+    /// annotate up to 10 interesting peaks in the range @p vbegin to @pvend with their m/z values (using deisotoping and intensity filtering)
+    void drawMZAtInterestingPeaks_(QPainter& painter, Plot1DCanvas* canvas, MSSpectrum::ConstIterator vbegin, MSSpectrum::ConstIterator vend);
+
+    const LayerDataPeak* layer_; ///< the data to paint
+  };
+
+} // namespace OpenMS

src/openms_gui/include/OpenMS/VISUAL/Plot1DCanvas.h

@@ -39,7 +39,9 @@
 
 // OpenMS
 #include <OpenMS/VISUAL/PlotCanvas.h>
+#include <OpenMS/VISUAL/Painter1DBase.h>
 
+// QT
 #include <QTextDocument>
 
 // STL
@@ -51,6 +53,7 @@ class QAction;
 
 namespace OpenMS
 {
+
   /**
       @brief Canvas for visualization of one or several spectra.
 
@@ -157,20 +160,13 @@ namespace OpenMS
     /// Add an annotation item for the given peak
     Annotation1DItem* addPeakAnnotation(const PeakIndex& peak_index, const QString& text, const QColor& color);
 
-    /// Draws all annotation items of @p layer_index on @p painter
-    void drawAnnotations(Size layer_index, QPainter& painter);
-
     /// ----- Alignment
-
     /// Performs an alignment of the layers with @p layer_index_1 and @p layer_index_2
     void performAlignment(Size layer_index_1, Size layer_index_2, const Param& param);
 
     /// Resets alignment_
     void resetAlignment();
 
-    /// Draws the alignment on @p painter
-    void drawAlignment(QPainter& painter);
-
     /// Returns the number of aligned pairs of peaks
     Size getAlignmentSize();
 
@@ -248,9 +244,9 @@ protected slots:
     void drawCoordinates_(QPainter& painter, const PeakIndex& peak);
     /// Draws the coordinates (or coordinate deltas) to the widget's upper left corner
     void drawDeltas_(QPainter& painter, const PeakIndex& start, const PeakIndex& end);
-
-    /// annotate interesting peaks in visible area with m/z
-    void drawMZAtInterestingPeaks_(Size layer_index, QPainter& painter);
+    
+    /// Draws the alignment on @p painter
+    void drawAlignment_(QPainter& painter);
 
     /**
         @brief Changes visible area interval
@@ -262,9 +258,6 @@ protected slots:
     /// Draws a highlighted peak; if draw_elongation is true, the elongation line is drawn (for measuring)
     void drawHighlightedPeak_(Size layer_index, const PeakIndex& peak, QPainter& painter, bool draw_elongation = false);
 
-    /// Draws a dashed line using the highlighted peak color parameter
-    void drawDashedLine_(const QPoint& from, const QPoint& to, QPainter& painter);
-
     /// Recalculates the current scale factor based on the specified layer (= 1.0 if intensity mode != IM_PERCENTAGE)
     void updatePercentageFactor_(Size layer_index);
 
@@ -353,6 +346,9 @@ protected slots:
     void translateRight_(Qt::KeyboardModifiers m) override;
     //docu in base class
     void paintGridLines_(QPainter& painter) override;
+
+    friend class Painter1DPeak;
+
   };
 } // namespace OpenMS
 

src/openms_gui/include/OpenMS/VISUAL/sources.cmake

@@ -30,6 +30,7 @@ MetaDataBrowser.h
 MultiGradient.h
 MultiGradientSelector.h
 OutputDirectory.h
+Painter1DBase.h
 ParamEditor.h
 Plot1DCanvas.h
 Plot1DWidget.h

src/openms_gui/source/VISUAL/LayerDataBase.cpp

@@ -97,13 +97,6 @@ namespace OpenMS
     }
   }
 
-
-  /// add annotation from an OSW sqlite file.
-
-
-  /// get annotation (e.g. to build a hierachical ID View)
-  /// Not const, because we might have incomplete data, which needs to be loaded from sql source
-
   LayerDataBase::OSWDataSharedPtrType& LayerDataBase::getChromatogramAnnotation()
   {
     return chrom_annotation_;
@@ -153,7 +146,6 @@ namespace OpenMS
     return cached_spectrum_;
   }
 
-  /// Returns a const-copy of the required spectrum which is guaranteed to be populated with raw data
 
   const LayerDataBase::ExperimentType::SpectrumType LayerDataBase::getSpectrum(Size spectrum_idx) const
   {