Changeset 9963

Timestamp:

09/13/13 14:42:38 (9 years ago)

Author:

bburlacu

Message:

#1772: Merged changes from the trunk and other branches. Added new ExtendedSymbolicExpressionTreeCanvas control for the visual exploration of tree genealogies. Reorganized some files and folders.

Location:

branches/HeuristicLab.EvolutionaryTracking

Files:

• HeuristicLab.Encodings.SymbolicExpressionTreeEncoding.Views/3.4/HeuristicLab.Encodings.SymbolicExpressionTreeEncoding.Views-3.4.csproj (modified) (2 diffs)
• HeuristicLab.Encodings.SymbolicExpressionTreeEncoding.Views/3.4/SymbolicExpressionTreeChart.cs (modified) (6 diffs)
• HeuristicLab.Encodings.SymbolicExpressionTreeEncoding.Views/3.4/TreeLayout.cs (deleted)
• HeuristicLab.Encodings.SymbolicExpressionTreeEncoding/3.4/Formatters/SymbolicExpressionTreeLatexFormatter.cs (added)
• HeuristicLab.Encodings.SymbolicExpressionTreeEncoding/3.4/HeuristicLab.Encodings.SymbolicExpressionTreeEncoding-3.4.csproj (modified) (4 diffs)
• HeuristicLab.Encodings.SymbolicExpressionTreeEncoding/3.4/Interfaces/ILayoutAdapter.cs (added)
• HeuristicLab.Encodings.SymbolicExpressionTreeEncoding/3.4/Interfaces/ILayoutNode.cs (added)
• HeuristicLab.Encodings.SymbolicExpressionTreeEncoding/3.4/LayoutEngines (added)
• HeuristicLab.Encodings.SymbolicExpressionTreeEncoding/3.4/LayoutEngines/LayoutNode.cs (added)
• HeuristicLab.Encodings.SymbolicExpressionTreeEncoding/3.4/LayoutEngines/ReingoldTilfordLayoutEngine.cs (added)
• HeuristicLab.Encodings.SymbolicExpressionTreeEncoding/3.4/LayoutEngines/SymbolicExpressionTreeLayoutAdapter.cs (added)
• HeuristicLab.EvolutionaryTracking.Views/3.4/AncestryLayoutAdapter.cs (added)
• HeuristicLab.EvolutionaryTracking.Views/3.4/ExtendedSymbolicExpressionTreeCanvas.cs (added)
• HeuristicLab.EvolutionaryTracking.Views/3.4/GenealogyGraphChart.cs (modified) (7 diffs)
• HeuristicLab.EvolutionaryTracking.Views/3.4/GenealogyGraphView.cs (modified) (1 diff)
• HeuristicLab.EvolutionaryTracking.Views/3.4/HeuristicLab.EvolutionaryTracking.Views-3.4.csproj (modified) (4 diffs)
• HeuristicLab.EvolutionaryTracking.Views/3.4/HeuristicLab.EvolutionaryTracking.Views-3.4.csproj.user (added)
• HeuristicLab.EvolutionaryTracking.Views/3.4/LineageExplorerView.Designer.cs (modified) (6 diffs)
• HeuristicLab.EvolutionaryTracking.Views/3.4/LineageExplorerView.cs (modified) (5 diffs)
• HeuristicLab.EvolutionaryTracking.Views/3.4/Primitives (added)
• HeuristicLab.EvolutionaryTracking.Views/3.4/Primitives/LabeledEllipse.cs (added)
• HeuristicLab.EvolutionaryTracking.Views/3.4/Primitives/LabeledRectangle.cs (added)
• HeuristicLab.EvolutionaryTracking.Views/3.4/Primitives/PrimitiveGroup.cs (added)
• HeuristicLab.EvolutionaryTracking.Views/3.4/VisualGenealogyGraphNode.cs (modified) (1 diff)
• HeuristicLab.EvolutionaryTracking.Views/3.4/VisualGenealogyGraphTextLabel.cs (modified) (3 diffs)
• HeuristicLab.EvolutionaryTracking/3.4/Analyzers/SymbolicDataAnalysisSolutionPruningOptimizer.cs (added)
• HeuristicLab.EvolutionaryTracking/3.4/Analyzers/SymbolicExpressionTreeEvolvabilityAnalyzer.cs (modified) (2 diffs)
• HeuristicLab.EvolutionaryTracking/3.4/Analyzers/SymbolicExpressionTreePruningAnalyzer.cs (added)
• HeuristicLab.EvolutionaryTracking/3.4/HeuristicLab.EvolutionaryTracking-3.4.csproj (modified) (2 diffs)
• HeuristicLab.EvolutionaryTracking/3.4/Interfaces/ISymbolicExpressionTreeGenealogyGraph.cs (modified) (1 diff)
• HeuristicLab.EvolutionaryTracking/3.4/Operators/SymbolicExpressionTreeGenealogyGraphBuilder.cs (modified) (3 diffs)
• HeuristicLab.EvolutionaryTracking/3.4/SymbolicExpressionTreeGenealogyGraph (added)
• HeuristicLab.EvolutionaryTracking/3.4/SymbolicExpressionTreeGenealogyGraph.cs (deleted)
• HeuristicLab.EvolutionaryTracking/3.4/SymbolicExpressionTreeGenealogyGraph/SymbolicExpressionTreeGenealogyGraph.cs (added)
• HeuristicLab.EvolutionaryTracking/3.4/SymbolicExpressionTreeGenealogyGraph/SymbolicExpressionTreeGenealogyGraphNode.cs (added)
• HeuristicLab.Optimization.Views/3.3/HeuristicLab.Optimization.Views-3.3.csproj (modified) (1 diff)
• HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Crossovers/SymbolicDataAnalysisExpressionStructuralSimilarityCrossover.cs (added)
• HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/HeuristicLab.Problems.DataAnalysis.Symbolic-3.4.csproj (modified) (1 diff)
• HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/SlidingWindow/SlidingWindowData.cs (modified) (1 diff)
• HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/SymbolicDataAnalysisSolutionPruningOptimizer.cs (added)
• HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/SymbolicDataAnalysisSolutionValuesCalculator.cs (deleted)

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.Encodings.SymbolicExpressionTreeEncoding.Views/3.4/HeuristicLab.Encodings.SymbolicExpressionTreeEncoding.Views-3.4.csproj

@@ -230 +230 @@
       <DependentUpon>SymbolicExpressionView.cs</DependentUpon>
     </Compile>
-    <Compile Include="TreeLayout.cs" />
     <Compile Include="VisualSymbolicExpressionTreeNode.cs" />
     <Compile Include="VisualSymbolicExpressionTreeNodeConnection.cs" />
@@ -267 +266 @@
       <Install>true</Install>
     </BootstrapperPackage>
-  </ItemGroup>
-  <ItemGroup>
-    <EmbeddedResource Include="SymbolicExpressionTreeChart.resx">
-      <DependentUpon>SymbolicExpressionTreeChart.cs</DependentUpon>
-    </EmbeddedResource>
   </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.Encodings.SymbolicExpressionTreeEncoding.Views/3.4/SymbolicExpressionTreeChart.cs

@@ -24 +24 @@
 using System.Drawing;
 using System.Drawing.Imaging;
+using System.IO;
+using System.Linq;
 using System.Windows.Forms;
 using Point = System.Drawing.Point;
@@ -33 +35 @@
     private Dictionary<ISymbolicExpressionTreeNode, VisualSymbolicExpressionTreeNode> visualTreeNodes;
     private Dictionary<Tuple<ISymbolicExpressionTreeNode, ISymbolicExpressionTreeNode>, VisualSymbolicExpressionTreeNodeConnection> visualLines;
+    private readonly ReingoldTilfordLayoutEngine<ISymbolicExpressionTreeNode> layoutEngine = new ReingoldTilfordLayoutEngine<ISymbolicExpressionTreeNode> { MinHorizontalSpacing = 5, MinVerticalSpacing = 5 };
+    private readonly SymbolicExpressionTreeLayoutAdapter layoutAdapter = new SymbolicExpressionTreeLayoutAdapter();
+
 
     public SymbolicExpressionTreeChart() {
@@ -160 +165 @@
         graphics.Clear(backgroundColor);
         if (tree != null) {
-          int height = this.Height / tree.Depth;
-          DrawFunctionTree(tree, graphics, 0, 0, this.Width, height);
+          DrawFunctionTree(tree, graphics, 70, 46, 20, 50);
         }
       }
@@ -254 +258 @@
     #region methods for painting the symbolic expression tree
 
-    private void DrawFunctionTree(ISymbolicExpressionTree tree, Graphics graphics, int x, int y, int width, int height) {
-      //      DrawFunctionTree(tree.Root, graphics, x, y, width, height, Point.Empty);
-      AlternateDraw(tree, graphics, 70, 46, 20, 50);
-    }
-
-    private void AlternateDraw(ISymbolicExpressionTree tree, Graphics graphics, int preferredWidth, int preferredHeight, int minDistance, int maxDistance) {
-      var tl = new TreeLayout();
-      tl.Distance = 5;
-      tl.SymbolicExpressionTree = tree;
-
-      var nodePositions = tl.GetNodeCoordinates();
-      var bounds = tl.Bounds();
+    private void DrawFunctionTree(ISymbolicExpressionTree tree, Graphics graphics, int preferredWidth, int preferredHeight, int minDistance, int maxDistance) {
+      var layoutNodes = layoutAdapter.Convert(tree).ToList();
+      layoutEngine.Reset();
+      layoutEngine.Root = layoutNodes[0];
+      foreach (var ln in layoutNodes)
+        layoutEngine.AddNode(ln.Content, ln);
+      layoutEngine.CalculateLayout();
+      var nodePositions = layoutEngine.GetNodeCoordinates();
+      var bounds = layoutEngine.Bounds();
 
       double sx = Width / bounds.Width;
       double sy = Height / bounds.Height;
 
-      double dx = tl.Distance * sx; // scaled horizontal distance
-      double dy = tl.Distance * sy; // scaled vertical distance
+      double dx = layoutEngine.MinHorizontalSpacing * sx; // scaled horizontal distance
+      double dy = layoutEngine.MinVerticalSpacing * sy; // scaled vertical distance
 
       int maxWidth = (int)Math.Round(dx);
@@ -307 +308 @@
             graphics.DrawLine(linePen, origin, target);
           }
-        }
-      }
-    }
-
-    /// <summary>
-    /// 
-    /// </summary>
-    /// <param name="node">the root of the function tree to draw</param>
-    /// <param name="graphics">graphics object to draw on</param>
-    /// <param name="x">x coordinate of drawing area</param>
-    /// <param name="y">y coordinate of drawing area</param>
-    /// <param name="width">width of drawing area</param>
-    /// <param name="height">height of drawing area</param>
-    private void DrawFunctionTree(ISymbolicExpressionTreeNode node, Graphics graphics, int x, int y, int width, int height, Point connectionPoint) {
-      VisualSymbolicExpressionTreeNode visualTreeNode = visualTreeNodes[node];
-      float center_x = x + width / 2;
-      float center_y = y + height / 2;
-      int actualWidth = width - spacing;
-      int actualHeight = height - spacing;
-
-      using (var textBrush = new SolidBrush(visualTreeNode.TextColor))
-      using (var nodeLinePen = new Pen(visualTreeNode.LineColor))
-      using (var nodeFillBrush = new SolidBrush(visualTreeNode.FillColor)) {
-
-        //calculate size of node
-        if (actualWidth >= visualTreeNode.PreferredWidth && actualHeight >= visualTreeNode.PreferredHeight) {
-          visualTreeNode.Width = visualTreeNode.PreferredWidth;
-          visualTreeNode.Height = visualTreeNode.PreferredHeight;
-          visualTreeNode.X = (int)center_x - visualTreeNode.Width / 2;
-          visualTreeNode.Y = (int)center_y - visualTreeNode.Height / 2;
-        }
-          //width too small to draw in desired sized
-        else if (actualWidth < visualTreeNode.PreferredWidth && actualHeight >= visualTreeNode.PreferredHeight) {
-          visualTreeNode.Width = actualWidth;
-          visualTreeNode.Height = visualTreeNode.PreferredHeight;
-          visualTreeNode.X = x;
-          visualTreeNode.Y = (int)center_y - visualTreeNode.Height / 2;
-        }
-          //height too small to draw in desired sized
-        else if (actualWidth >= visualTreeNode.PreferredWidth && actualHeight < visualTreeNode.PreferredHeight) {
-          visualTreeNode.Width = visualTreeNode.PreferredWidth;
-          visualTreeNode.Height = actualHeight;
-          visualTreeNode.X = (int)center_x - visualTreeNode.Width / 2;
-          visualTreeNode.Y = y;
-        }
-          //width and height too small to draw in desired size
-        else {
-          visualTreeNode.Width = actualWidth;
-          visualTreeNode.Height = actualHeight;
-          visualTreeNode.X = x;
-          visualTreeNode.Y = y;
-        }
-
-        //draw terminal node
-        if (node.SubtreeCount == 0) {
-          graphics.FillRectangle(nodeFillBrush, visualTreeNode.X, visualTreeNode.Y, visualTreeNode.Width, visualTreeNode.Height);
-          graphics.DrawRectangle(nodeLinePen, visualTreeNode.X, visualTreeNode.Y, visualTreeNode.Width, visualTreeNode.Height);
-        } else {
-          graphics.FillEllipse(nodeFillBrush, visualTreeNode.X, visualTreeNode.Y, visualTreeNode.Width, visualTreeNode.Height);
-          graphics.DrawEllipse(nodeLinePen, visualTreeNode.X, visualTreeNode.Y, visualTreeNode.Width, visualTreeNode.Height);
-        }
-
-        //draw name of symbol
-        var text = node.ToString();
-        graphics.DrawString(text, textFont, textBrush, new RectangleF(visualTreeNode.X, visualTreeNode.Y, visualTreeNode.Width, visualTreeNode.Height), stringFormat);
-
-        //draw connection line to parent node
-        if (!connectionPoint.IsEmpty && node.Parent != null) {
-          var visualLine = GetVisualSymbolicExpressionTreeNodeConnection(node.Parent, node);
-          using (Pen linePen = new Pen(visualLine.LineColor)) {
-            linePen.DashStyle = visualLine.DashStyle;
-            graphics.DrawLine(linePen, connectionPoint, new Point(visualTreeNode.X + visualTreeNode.Width / 2, visualTreeNode.Y));
-          }
-        }
-
-        //calculate areas for the subtrees according to their tree size and call drawFunctionTree
-        Point connectFrom = new Point(visualTreeNode.X + visualTreeNode.Width / 2, visualTreeNode.Y + visualTreeNode.Height);
-        int[] xBoundaries = new int[node.SubtreeCount + 1];
-        xBoundaries[0] = x;
-        for (int i = 0; i < node.SubtreeCount; i++) {
-          xBoundaries[i + 1] = (int)(xBoundaries[i] + (width * (double)node.GetSubtree(i).GetLength()) / (node.GetLength() - 1));
-          DrawFunctionTree(node.GetSubtree(i), graphics, xBoundaries[i], y + height, xBoundaries[i + 1] - xBoundaries[i], height, connectFrom);
         }
       }
@@ -455 +374 @@
     }
     #endregion
+    #region export pgf/tikz
+    private void exportLatexToolStripMenuItem_Click(object sender, EventArgs e) {
+      using (var dialog = new SaveFileDialog { Filter = "Tex (*.tex)|*.tex" }) {
+        if (dialog.ShowDialog() != DialogResult.OK) return;
+        string filename = dialog.FileName.ToLower();
+        var formatter = new SymbolicExpressionTreeLatexFormatter();
+        File.WriteAllText(filename, formatter.Format(Tree));
+      }
+    }
+    #endregion
   }
 }

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.Encodings.SymbolicExpressionTreeEncoding/3.4/HeuristicLab.Encodings.SymbolicExpressionTreeEncoding-3.4.csproj

@@ -191 +191 @@
     <Compile Include="Crossovers\TracingSymbolicExpressionTreeCrossover.cs" />
     <Compile Include="Formatters\SymbolicExpressionTreeGraphvizFormatter.cs" />
+    <Compile Include="Formatters\SymbolicExpressionTreeLatexFormatter.cs" />
     <Compile Include="Fragment.cs" />
     <Compile Include="GenericWrapper.cs" />
     <Compile Include="GeneticExchange.cs" />
     <Compile Include="Interfaces\IFragment.cs" />
+    <Compile Include="Interfaces\ILayoutAdapter.cs" />
+    <Compile Include="Interfaces\ILayoutNode.cs" />
     <Compile Include="Interfaces\IReadOnlySymbol.cs" />
     <Compile Include="Interfaces\ISymbolicExpressionGrammar.cs" />
@@ -217 +220 @@
     <Compile Include="Interfaces\Operators\ISymbolicExpressionTreeSizeConstraintOperator.cs" />
     <Compile Include="Interfaces\Operators\ITracingSymbolicExpressionTreeOperator.cs" />
+    <Compile Include="LayoutEngines\LayoutNode.cs" />
+    <Compile Include="LayoutEngines\ReingoldTilfordLayoutEngine.cs" />
+    <Compile Include="LayoutEngines\SymbolicExpressionTreeLayoutAdapter.cs" />
     <Compile Include="Manipulators\ChangeNodeTypeManipulation.cs" />
     <Compile Include="Interfaces\Operators\ISymbolicExpressionTreeManipulator.cs" />
@@ -240 +246 @@
     <Compile Include="Interfaces\Operators\ISymbolicExpressionTreeOperator.cs" />
     <Compile Include="SymbolicExpressionTree.cs" />
-    <Compile Include="Properties\AssemblyInfo.cs" />
     <Compile Include="SymbolicExpressionTreeNode.cs" />
     <Compile Include="Symbols\Argument.cs" />
@@ -258 +263 @@
     <None Include="Plugin.cs.frame" />
     <None Include="Properties\AssemblyInfo.cs.frame" />
+    <Compile Include="Properties\AssemblyInfo.cs" />
   </ItemGroup>
   <ItemGroup>

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.EvolutionaryTracking.Views/3.4/GenealogyGraphChart.cs

@@ -111 +111 @@
         if (layers[i].Rank.IsAlmost(rank)) {
           var visualTextNode = new VisualGenealogyGraphTextLabel(Chart, x, y + 2, x + Diameter, y + Diameter) {
-            Brush = new SolidBrush(Color.Black),
+            FontBrush = new SolidBrush(Color.Black),
             Font = new Font("Arial", Diameter - 4, FontStyle.Regular, GraphicsUnit.Pixel),
             Text = String.Format("{0:0}", rank)
@@ -154 +154 @@
       }
       // add arcs separately (to avoid some ordering problems)
-      foreach (SymbolicExpressionGenealogyGraphNode node in Graph.Nodes) {
+      foreach (SymbolicExpressionTreeGenealogyGraphNode node in Graph.Nodes) {
         VisualGenealogyGraphNode visualNode = GetVisualGenealogyGraphNode(node);
         if (node.InEdges == null) continue;
@@ -171 +171 @@
 
       //        var brush = new SolidBrush(Color.BlueViolet);
-      //        visualGraphNode.Brush = brush;
+      //        visualGraphNode.FontBrush = brush;
       //      }
 
@@ -267 +267 @@
         arc.Pen.Brush = new LinearGradientBrush(start, end, source.GetColor(), target.GetColor());
         arc.Pen.Color = Color.Transparent;
-        //        arc.Pen.Brush = new SolidBrush(Color.DarkGray);
+        //        arc.Pen.FontBrush = new SolidBrush(Color.DarkGray);
         DrawLineage(nodeSelector(arc), arcSelector, nodeSelector);
       }
@@ -300 +300 @@
     }
 
-    public void HighlightNodes(IEnumerable<SymbolicExpressionGenealogyGraphNode> nodes) {
+    public void HighlightNodes(IEnumerable<SymbolicExpressionTreeGenealogyGraphNode> nodes) {
       Chart.UpdateEnabled = false;
       ClearAllNodes();
@@ -333 +333 @@
     }
 
-    public void HighlightNode(SymbolicExpressionGenealogyGraphNode graphNode, Color color) {
+    public void HighlightNode(SymbolicExpressionTreeGenealogyGraphNode graphNode, Color color) {
       GetVisualGenealogyGraphNode(graphNode).Brush = new SolidBrush(color);
     }
@@ -388 +388 @@
 
   internal static class Util {
-    public static Color GetColor(this SymbolicExpressionGenealogyGraphNode node) {
+    public static Color GetColor(this SymbolicExpressionTreeGenealogyGraphNode node) {
       var colorIndex = (int)(node.Quality * ColorGradient.Colors.Count);
       if (colorIndex >= ColorGradient.Colors.Count) --colorIndex;

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.EvolutionaryTracking.Views/3.4/GenealogyGraphView.cs

@@ -231 +231 @@
 
     private void highlightRootParentsButton_Click(object sender, EventArgs e) {
-      var nodes = genealogyGraphChart.Graph.Nodes.Where(n => n.InEdges != null && n.InEdges.Count == 2).Select(n => (SymbolicExpressionGenealogyGraphNode)n.InEdges[0].Source).ToList();
+      var nodes = genealogyGraphChart.Graph.Nodes.Where(n => n.InEdges != null && n.InEdges.Count == 2).Select(n => (SymbolicExpressionTreeGenealogyGraphNode)n.InEdges[0].Source).ToList();
       genealogyGraphChart.HighlightNodes(nodes);
     }
 
     private void highlightSecondaryParentsButton_Click(object sender, EventArgs e) {
-      var nodes = genealogyGraphChart.Graph.Nodes.Where(n => n.InEdges != null && n.InEdges.Count == 2).Select(n => (SymbolicExpressionGenealogyGraphNode)n.InEdges[1].Source).ToList();
+      var nodes = genealogyGraphChart.Graph.Nodes.Where(n => n.InEdges != null && n.InEdges.Count == 2).Select(n => (SymbolicExpressionTreeGenealogyGraphNode)n.InEdges[1].Source).ToList();
       genealogyGraphChart.HighlightNodes(nodes);
     }

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.EvolutionaryTracking.Views/3.4/HeuristicLab.EvolutionaryTracking.Views-3.4.csproj

@@ -109 +109 @@
   </ItemGroup>
   <ItemGroup>
+    <Compile Include="AncestryLayoutAdapter.cs" />
+    <Compile Include="ExtendedSymbolicExpressionTreeCanvas.cs">
+      <SubType>UserControl</SubType>
+    </Compile>
     <Compile Include="FrequentFragmentsDialog.cs">
       <SubType>Form</SubType>
@@ -133 +137 @@
       <DependentUpon>GenealogyGraphView.cs</DependentUpon>
     </Compile>
-    <Compile Include="Karyogram.cs">
-      <SubType>UserControl</SubType>
-    </Compile>
-    <Compile Include="Karyogram.Designer.cs">
-      <DependentUpon>Karyogram.cs</DependentUpon>
-    </Compile>
     <Compile Include="LineageExplorerView.cs">
       <SubType>UserControl</SubType>
@@ -146 +144 @@
     </Compile>
     <Compile Include="Plugin.cs" />
+    <Compile Include="Primitives\LabeledEllipse.cs" />
+    <Compile Include="Primitives\LabeledRectangle.cs" />
+    <Compile Include="Primitives\PrimitiveGroup.cs" />
     <Compile Include="Properties\AssemblyInfo.cs" />
     <Compile Include="Properties\Resources.Designer.cs">
@@ -182 +183 @@
   </ItemGroup>
   <ItemGroup>
-    <EmbeddedResource Include="FrequentFragmentsDialog.resx">
-      <DependentUpon>FrequentFragmentsDialog.cs</DependentUpon>
-    </EmbeddedResource>
-    <EmbeddedResource Include="GenealogyGraphDialog.resx">
-      <DependentUpon>GenealogyGraphDialog.cs</DependentUpon>
-    </EmbeddedResource>
-    <EmbeddedResource Include="GenealogyGraphView.resx">
-      <DependentUpon>GenealogyGraphView.cs</DependentUpon>
-    </EmbeddedResource>
-    <EmbeddedResource Include="LineageExplorerView.resx">
-      <DependentUpon>LineageExplorerView.cs</DependentUpon>
-    </EmbeddedResource>
     <EmbeddedResource Include="Properties\Resources.resx">
       <Generator>ResXFileCodeGenerator</Generator>

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.EvolutionaryTracking.Views/3.4/LineageExplorerView.Designer.cs

@@ -44 +44 @@
       this.consideredTrees = new System.Windows.Forms.Label();
       this.tabPage3 = new System.Windows.Forms.TabPage();
-      this.karyograph1 = new HeuristicLab.EvolutionaryTracking.Views.Karyogram();
       this.karyographTab.SuspendLayout();
       this.tabPage1.SuspendLayout();
@@ -91 +90 @@
       // qualityImprovementTreeView
       // 
-      this.qualityImprovementTreeView.Anchor = ((System.Windows.Forms.AnchorStyles)(((System.Windows.Forms.AnchorStyles.Top | System.Windows.Forms.AnchorStyles.Bottom) 
+      this.qualityImprovementTreeView.Anchor = ((System.Windows.Forms.AnchorStyles)(((System.Windows.Forms.AnchorStyles.Top | System.Windows.Forms.AnchorStyles.Bottom)
             | System.Windows.Forms.AnchorStyles.Right)));
       this.qualityImprovementTreeView.HideSelection = false;
@@ -102 +101 @@
       // symbolicExpressionTreeChart
       // 
-      this.symbolicExpressionTreeChart.Anchor = ((System.Windows.Forms.AnchorStyles)((((System.Windows.Forms.AnchorStyles.Top | System.Windows.Forms.AnchorStyles.Bottom) 
-            | System.Windows.Forms.AnchorStyles.Left) 
+      this.symbolicExpressionTreeChart.Anchor = ((System.Windows.Forms.AnchorStyles)((((System.Windows.Forms.AnchorStyles.Top | System.Windows.Forms.AnchorStyles.Bottom)
+            | System.Windows.Forms.AnchorStyles.Left)
             | System.Windows.Forms.AnchorStyles.Right)));
       this.symbolicExpressionTreeChart.BackgroundColor = System.Drawing.Color.White;
@@ -250 +249 @@
       // tabPage3
       // 
-      this.tabPage3.Controls.Add(this.karyograph1);
       this.tabPage3.Location = new System.Drawing.Point(4, 22);
       this.tabPage3.Name = "tabPage3";
@@ -258 +256 @@
       this.tabPage3.Text = "Karyograph";
       this.tabPage3.UseVisualStyleBackColor = true;
-      // 
-      // karyograph1
-      // 
-      this.karyograph1.BackColor = System.Drawing.SystemColors.Control;
-      this.karyograph1.Chart = null;
-      this.karyograph1.Dock = System.Windows.Forms.DockStyle.Fill;
-      this.karyograph1.Location = new System.Drawing.Point(3, 3);
-      this.karyograph1.Name = "karyograph1";
-      this.karyograph1.ScaleOnResize = true;
-      this.karyograph1.Size = new System.Drawing.Size(1002, 637);
-      this.karyograph1.TabIndex = 0;
       // 
       // LineageExplorerView
@@ -311 +298 @@
     private System.Windows.Forms.Panel panel4;
     private System.Windows.Forms.TabPage tabPage3;
-    private Karyogram karyograph1;
-
-
-
-
-
-
-
   }
 }

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.EvolutionaryTracking.Views/3.4/LineageExplorerView.cs

@@ -16 +16 @@
   public sealed partial class LineageExplorerView : ItemView {
     private Dictionary<TreeNode, ISymbolicExpressionTree> treeMap;
-    private List<SymbolicExpressionGenealogyGraphNode> lineage;
+    private List<SymbolicExpressionTreeGenealogyGraphNode> lineage;
 
     private Dictionary<ISymbolicExpressionTree, Dictionary<ISymbolicExpressionTreeNode, double>> fragmentFrequencies;
@@ -59 +59 @@
         }
       }
-
-      karyograph1.Trees = Content.Trees.OrderByDescending(x => x.Item2).Select(x => x.Item1).ToList();
     }
 
@@ -94 +92 @@
 
       var graphNode = Content.GenealogyGraph.GetGraphNodes(symbExprTree).Last();
-      lineage = lineage ?? new List<SymbolicExpressionGenealogyGraphNode>();
+      lineage = lineage ?? new List<SymbolicExpressionTreeGenealogyGraphNode>();
       lineage.Clear();
       lineage.Add(graphNode);
@@ -100 +98 @@
       var gn = graphNode;
       while (gn.InEdges != null && gn.InEdges.Count != 0) {
-        gn = (SymbolicExpressionGenealogyGraphNode)gn.InEdges[0].Source;
+        gn = (SymbolicExpressionTreeGenealogyGraphNode)gn.InEdges[0].Source;
         lineage.Add(gn);
       }
@@ -127 +125 @@
       symbolicExpressionTreeChart.Tree = symbExprTree;
       var matchingNodes = Content.GenealogyGraph.GetGraphNodes(symbExprTree);
-      SymbolicExpressionGenealogyGraphNode graphNode = matchingNodes.First();
+      SymbolicExpressionTreeGenealogyGraphNode graphNode = matchingNodes.First();
       if (graphNode.InEdges == null) {
         symbolicExpressionTreeChart.SuspendRepaint = false;

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.EvolutionaryTracking.Views/3.4/VisualGenealogyGraphNode.cs

@@ -27 +27 @@
 namespace HeuristicLab.EvolutionaryTracking.Views {
   public class VisualGenealogyGraphNode : Ellipse {
-    public SymbolicExpressionGenealogyGraphNode Data { get; internal set; }
+    public SymbolicExpressionTreeGenealogyGraphNode Data { get; internal set; }
     private List<VisualGenealogyGraphArc> incomingArcs = new List<VisualGenealogyGraphArc>();
     private List<VisualGenealogyGraphArc> outgoingArcs = new List<VisualGenealogyGraphArc>();

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.EvolutionaryTracking.Views/3.4/VisualGenealogyGraphTextLabel.cs

@@ -1 @@
-using System;
-using System.Drawing;
+using System.Drawing;
 using HeuristicLab.Visualization;
 using Rectangle = HeuristicLab.Visualization.Rectangle;
@@ -12 +11 @@
     public Font Font { get { return font; } set { font = value; } }
 
-    private Brush brush;
-    public Brush Brush { get { return brush; } set { brush = value; } }
+    private Brush fontBrush;
+    public Brush FontBrush { get { return fontBrush; } set { fontBrush = value; } }
 
     public VisualGenealogyGraphTextLabel(IChart chart, PointD lowerLeft, PointD upperRight)
@@ -34 +33 @@
       float fontSize = s.Height;
       font = new Font(font.Name, fontSize, Font.Style, GraphicsUnit.Pixel);
-      graphics.DrawString(text, font, brush, p.X, p.Y);
+      graphics.DrawString(text, font, fontBrush, p.X, p.Y);
     }
 
-    public EventHandler Update;
-    protected virtual void OnUpdate() {
-      if ((UpdateEnabled) && (Update != null)) {
-        Update(this, new EventArgs());
+    protected override void OnUpdate() {
+      if ((UpdateEnabled)) {
+        base.OnUpdate();
       }
-      base.OnUpdate();
     }
   }

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.EvolutionaryTracking/3.4/Analyzers/SymbolicExpressionTreeEvolvabilityAnalyzer.cs

@@ -159 +159 @@
                                where graphNode.InEdges.Count == 1
                                // mutation
-                               let source = (SymbolicExpressionGenealogyGraphNode)graphNode.InEdges[0].Source
+                               let source = (SymbolicExpressionTreeGenealogyGraphNode)graphNode.InEdges[0].Source
                                where graphNode.SymbolicExpressionTree != source.SymbolicExpressionTree // skip elites
                                select source).ToList();
@@ -177 +177 @@
           switch (graphNode.InEdges.Count) {
             case 2: {
-                parentQuality = graphNode.InEdges.Max(e => ((SymbolicExpressionGenealogyGraphNode)e.Source).Quality);
+                parentQuality = graphNode.InEdges.Max(e => ((SymbolicExpressionTreeGenealogyGraphNode)e.Source).Quality);
                 crossoverImprovements.Add(quality - parentQuality);
                 break;
               }
             case 1: {
-                parentQuality = graphNode.InEdges.Max(e => ((SymbolicExpressionGenealogyGraphNode)e.Source).Quality);
+                parentQuality = graphNode.InEdges.Max(e => ((SymbolicExpressionTreeGenealogyGraphNode)e.Source).Quality);
                 if (ConstantOptimizationIntermediateParents.Value && ConstantOptimizationEvaluator != null) {
 
                   //Get the optimized fitness of the intermediate parent (without actually updating the constants in the tree)
-                  var intermediateParent = ((SymbolicExpressionGenealogyGraphNode)graphNode.InEdges[0].Source).SymbolicExpressionTree;
+                  var intermediateParent = ((SymbolicExpressionTreeGenealogyGraphNode)graphNode.InEdges[0].Source).SymbolicExpressionTree;
                   parentQuality = Evaluate(intermediateParent, ConstantOptimizationEvaluator);
                 }

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.EvolutionaryTracking/3.4/HeuristicLab.EvolutionaryTracking-3.4.csproj

@@ -131 +131 @@
   </ItemGroup>
   <ItemGroup>
-    <Compile Include="Analyzers\BuildingBlocks\BuildingBlockHistoryAnalyzer.cs" />
     <Compile Include="Analyzers\BuildingBlocks\RelevantBuildingBlocksAnalyzer.cs" />
     <Compile Include="Analyzers\BuildingBlocks\Poly10BuildingBlocksAnalyzer.cs" />
-    <Compile Include="Analyzers\LineageRetrofittingAnalyzer.cs" />
     <Compile Include="Analyzers\SymbolicExpressionTreePruningAnalyzer.cs" />
     <Compile Include="Analyzers\SymbolicExpressionTreeShapeAnalyzer.cs" />
@@ -162 +160 @@
     <Compile Include="Properties\AssemblyInfo.cs" />
     <Compile Include="SymbolGraph.cs" />
-    <Compile Include="SymbolicExpressionTreeGenealogyGraph.cs" />
+    <Compile Include="SymbolicExpressionTreeGenealogyGraph\SymbolicExpressionTreeGenealogyGraph.cs" />
+    <Compile Include="SymbolicExpressionTreeGenealogyGraph\SymbolicExpressionTreeGenealogyGraphNode.cs" />
   </ItemGroup>
   <ItemGroup />

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.EvolutionaryTracking/3.4/Interfaces/ISymbolicExpressionTreeGenealogyGraph.cs

@@ -24 +24 @@
 
 namespace HeuristicLab.EvolutionaryTracking {
-  public interface ISymbolicExpressionTreeGenealogyGraph : IGenericGraph<SymbolicExpressionGenealogyGraphNode> {
-    List<SymbolicExpressionGenealogyGraphNode> GetGraphNodes(ISymbolicExpressionTree tree);
+  public interface ISymbolicExpressionTreeGenealogyGraph : IGenericGraph<SymbolicExpressionTreeGenealogyGraphNode> {
+    List<SymbolicExpressionTreeGenealogyGraphNode> GetGraphNodes(ISymbolicExpressionTree tree);
   }
 }

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.EvolutionaryTracking/3.4/Operators/SymbolicExpressionTreeGenealogyGraphBuilder.cs

@@ -214 +214 @@
           var tree = pair.Tree;
           var quality = pair.Quality;
-          graph.AddNode(new SymbolicExpressionGenealogyGraphNode {
+          graph.AddNode(new SymbolicExpressionTreeGenealogyGraphNode {
             SymbolicExpressionTree = tree,
             Quality = quality,
@@ -226 +226 @@
                         let tree = pairs[i].Tree
                         let quality = pairs[i].Quality
-                        select new SymbolicExpressionGenealogyGraphNode {
+                        select new SymbolicExpressionTreeGenealogyGraphNode {
                           SymbolicExpressionTree = tree,
                           Quality = quality,
@@ -240 +240 @@
          // 1 parent means mutation
          let p = (ISymbolicExpressionTree)parents[0]
-         select new SymbolicExpressionGenealogyGraphNode {
+         select new SymbolicExpressionTreeGenealogyGraphNode {
            SymbolicExpressionTree = p,
            Quality = Evaluate(p),

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.Optimization.Views/3.3/HeuristicLab.Optimization.Views-3.3.csproj

@@ -390 +390 @@
     </BootstrapperPackage>
   </ItemGroup>
-  <ItemGroup>
-    <EmbeddedResource Include="RunCollectionViews\RunCollectionDataTableView.resx">
-      <DependentUpon>RunCollectionDataTableView.cs</DependentUpon>
-    </EmbeddedResource>
-  </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/HeuristicLab.Problems.DataAnalysis.Symbolic-3.4.csproj

@@ -240 +240 @@
     <Compile Include="SymbolicDataAnalysisProblem.cs" />
     <Compile Include="SymbolicDataAnalysisSolutionImpactValuesCalculator.cs" />
+    <Compile Include="SymbolicDataAnalysisSolutionPruningOptimizer.cs" />
     <Compile Include="SymbolicDataAnalysisSolutionTextRenderer.cs" />
     <Compile Include="Symbols\Addition.cs" />

branches/HeuristicLab.EvolutionaryTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/SlidingWindow/SlidingWindowData.cs

@@ -61 +61 @@
       : base(original, cloner) {
       slidingWindowPosition = cloner.Clone(original.slidingWindowPosition);
-      targetValues = new List<double>(original.targetValues);
+      if (original.targetValues != null)
+        targetValues = new List<double>(original.targetValues);
+      if (original.estimatedValues != null)
+        estimatedValues = new List<double>(original.estimatedValues);
     }
     public override IDeepCloneable Clone(Cloner cloner) {