Annotation bugfix and extra heatmap

PL2/PL2-gui/src/main/java/nl/tudelft/pl2016gr2/gui/view/AnnotationSearchPaneController.java

@@ -64,7 +64,7 @@ private void initializeTable() {
             // annotations in the graph
             selectionManager.select(new ViewAnnotation(selection, selectionManager));
             graphPaneController.centerOnLevel(
-                selection.getStartInGraph());
+                selection.start);
           }
         }
     );

PL2/PL2-gui/src/main/java/nl/tudelft/pl2016gr2/gui/view/graph/GraphPaneController.java

@@ -27,6 +27,7 @@
 import javafx.scene.layout.AnchorPane;
 import javafx.scene.layout.Pane;
 import javafx.scene.layout.Region;
+import javafx.scene.paint.Color;
 import javafx.scene.shape.Rectangle;
 import nl.tudelft.pl2016gr2.core.algorithms.subgraph.GraphOrdererThread;
 import nl.tudelft.pl2016gr2.core.algorithms.subgraph.OrderedGraph;
@@ -35,6 +36,7 @@
 import nl.tudelft.pl2016gr2.gui.view.graph.heatmap.IHeatmapColorer;
 import nl.tudelft.pl2016gr2.gui.view.graph.heatmap.IndelDensity;
 import nl.tudelft.pl2016gr2.gui.view.graph.heatmap.MutationDensity;
+import nl.tudelft.pl2016gr2.gui.view.graph.heatmap.NoOverlapHeatmap;
 import nl.tudelft.pl2016gr2.gui.view.graph.heatmap.OverlapHeatmap;
 import nl.tudelft.pl2016gr2.gui.view.graph.heatmap.PhyloBubbleDensity;
 import nl.tudelft.pl2016gr2.gui.view.graph.heatmap.PointMutationDensity;
@@ -226,6 +228,8 @@ private void addHeatmapOptions() {
     heatmapOptions.put("Graph based bubbles", new GraphBubbleDensity(heatmapGraphics, zoomFactor));
     heatmapOptions.put("Equalities between the graphs (dark = equal, light = not equal",
         new OverlapHeatmap(heatmapGraphics, zoomFactor));
+    heatmapOptions.put("Differences between the graphs (dark = not equal, light = equal",
+        new NoOverlapHeatmap(heatmapGraphics, zoomFactor));
   }
 
   /**
@@ -734,8 +738,8 @@ private void clearCanvas() {
         topEdgeCanvas.getWidth());
     bottomEdgeCanvas.getGraphicsContext2D().clearRect(0, 0, bottomEdgeCanvas.getWidth(),
         bottomEdgeCanvas.getWidth());
-    heatmap.getGraphicsContext2D().clearRect(0, 0, heatmap.getWidth(),
-        heatmap.getHeight());
+    heatmap.getGraphicsContext2D().setFill(Color.WHITE);
+    heatmap.getGraphicsContext2D().fillRect(0, 0, heatmap.getWidth(), heatmap.getHeight());
   }
 
   /**
@@ -865,7 +869,7 @@ private void drawAnnotationBox(GraphNode node, IViewGraphNode viewNode, Pane pan
     if (!node.hasAnnotations()) {
       return;
     }
-    boolean odd = false;
+    double previousEndPosition = Double.NEGATIVE_INFINITY;
     for (Annotation annotation : node.getAnnotations()) {
       double annotationStart = calcAnnotationStart(annotation, viewNode, startLevel);
       double annotationEnd = getAnnotationEnd(annotation, viewNode, startLevel);
@@ -876,11 +880,13 @@ private void drawAnnotationBox(GraphNode node, IViewGraphNode viewNode, Pane pan
       viewAnnotation.setLayoutY(viewNode.centerYProperty().get() - viewNode.getHeight() / 2.0);
       double maxHeight = viewNode.getHeight() / 2.0;
       viewAnnotation.setHeight(Math.min(maxHeight, ANNOTATION_HEIGHT));
-      viewAnnotation.setOddOffset(odd);
-
+      if (annotationStart < previousEndPosition) {
+        viewAnnotation.setOddOffset();
+      } else {
+        previousEndPosition = annotationEnd;
+      }
       pane.getChildren().add(viewAnnotation);
       viewAnnotation.addLabel(pane);
-      odd = !odd;
     }
   }
 

PL2/PL2-gui/src/main/java/nl/tudelft/pl2016gr2/gui/view/graph/ViewAnnotation.java

@@ -61,14 +61,10 @@ public void addLabel(Pane pane) {
   }
 
   /**
-   * Sets a vertical offset if this label is the nth label of a node, where n is odd.
-   *
-   * @param setOffset if this is an odd node.
+   * Sets a vertical offset to this label so if doesn't overlap with a different label.
    */
-  public void setOddOffset(boolean setOffset) {
-    if (setOffset) {
-      setLayoutY(getLayoutY() + getHeight());
-    }
+  public void setOddOffset() {
+    setLayoutY(getLayoutY() + getHeight());
   }
 
   @Override

PL2/PL2-gui/src/main/java/nl/tudelft/pl2016gr2/gui/view/graph/heatmap/NoOverlapHeatmap.java

@@ -0,0 +1,35 @@
+package nl.tudelft.pl2016gr2.gui.view.graph.heatmap;
+
+import static nl.tudelft.pl2016gr2.gui.view.graph.heatmap.OverlapHeatmap.NO_OVERLAP_COLOR;
+import static nl.tudelft.pl2016gr2.gui.view.graph.heatmap.OverlapHeatmap.OVERLAP_COLOR;
+
+import javafx.beans.value.ObservableDoubleValue;
+import javafx.scene.canvas.GraphicsContext;
+import nl.tudelft.pl2016gr2.model.graph.nodes.SequenceNode;
+
+/**
+ * This is a heatmap which indicates the positions of all of the non overlapping nodes (nodes which
+ * are not in both the top and bottom graph).
+ *
+ * @author Faris
+ */
+public class NoOverlapHeatmap extends AbstractHeatmap {
+
+  public NoOverlapHeatmap(GraphicsContext heatmapGraphics, ObservableDoubleValue zoomFactor) {
+    super(heatmapGraphics, zoomFactor);
+  }
+
+  @Override
+  protected double getWidthMultiplier() {
+    return 1.0;
+  }
+
+  @Override
+  public void visit(SequenceNode node) {
+    if (node.getGuiData().overlapping) {
+      setColor(NO_OVERLAP_COLOR);
+    } else {
+      setColor(OVERLAP_COLOR);
+    }
+  }
+}

PL2/PL2-gui/src/main/java/nl/tudelft/pl2016gr2/gui/view/graph/heatmap/OverlapHeatmap.java

@@ -13,8 +13,8 @@
  */
 public class OverlapHeatmap extends AbstractHeatmap {
 
-  private static final Color OVERLAP_COLOR = Color.rgb(0, 0, 0, 0.2);
-  private static final Color NO_OVERLAP_COLOR = Color.rgb(255, 255, 255, 0.2);
+  public static final Color OVERLAP_COLOR = Color.rgb(0, 0, 0, 0.2);
+  public static final Color NO_OVERLAP_COLOR = Color.rgb(255, 255, 255, 0.2);
 
   public OverlapHeatmap(GraphicsContext heatmapGraphics, ObservableDoubleValue zoomFactor) {
     super(heatmapGraphics, zoomFactor);