Merge branch 'joswinter-knownMutations' into demo

Author: alangerak

lifetiles-core/src/main/resources/settings/lifetiles.conf

@@ -2,3 +2,5 @@
 empty_segments = false
 mutations = true
 num_vertices_bucket = 50
+bookmark_radius = 25
+bookmark_opacity = 0.35

lifetiles-graph/src/main/java/nl/tudelft/lifetiles/graph/controller/GraphController.java

@@ -405,6 +405,7 @@ private void repaintPosition(final double position) {
             if (currEndPosition != endBucket
                     && currStartPosition != startBucket || repaintNow) {
                 Group graphDrawing = new Group();
+                graphDrawing.setManaged(false);
                 graphDrawing.getChildren().add(
                         drawGraph(startBucket, endBucket));
                 graphDrawing.getChildren().add(

lifetiles-graph/src/main/java/nl/tudelft/lifetiles/graph/view/Bookmark.java

@@ -2,27 +2,38 @@
 
 import javafx.scene.control.Tooltip;
 import javafx.scene.paint.Color;
-import javafx.scene.shape.Rectangle;
+import javafx.scene.shape.Circle;
 import nl.tudelft.lifetiles.annotation.model.KnownMutation;
+import nl.tudelft.lifetiles.core.util.Settings;
 
 /**
  * A bookmark is the equivalent of a known mutation mapped onto the graph.
  *
  * @author Jos
  *
  */
-public class Bookmark extends Rectangle {
+public class Bookmark extends Circle {
 
     /**
      * The standard opacity of the bookmark overlay.
      */
-    private static final double OPACITY = 0.5;
+    private static final double OPACITY = Double.parseDouble(Settings.get("bookmark_opacity"));
 
     /**
      * The standard color of the bookmark overlay.
      */
     private static final Color STANDARD_COLOR = Color.YELLOW;
 
+    /**
+     * The radius of the bookmark circle.
+     */
+    private static final double RADIUS = Double.parseDouble(Settings.get("bookmark_radius"));
+
+    /**
+     * Center of the segment so the origin of the circle is placed at the correct segment position.
+     */
+    private static final double SEGMENT_CENTER = 0.5;
+
     /**
      * Constructs a bookmark from a vertex, a annotation and a segment position.
      *
@@ -38,10 +49,10 @@ public class Bookmark extends Rectangle {
     public Bookmark(final VertexView vertex,
             final KnownMutation knownMutation, final long segmentPosition,
             final double scale) {
-        super(vertex.HORIZONTALSCALE * scale, vertex.getHeight());
-        setLayoutX(vertex.getLayoutX() + segmentPosition
+        super(RADIUS);
+        setLayoutX(vertex.getLayoutX() + (segmentPosition + SEGMENT_CENTER)
                 * vertex.HORIZONTALSCALE * scale);
-        setLayoutY(vertex.getLayoutY());
+        setLayoutY(vertex.getLayoutY() + vertex.getHeight() / 2);
         setOpacity(OPACITY);
         setFill(STANDARD_COLOR);
 

lifetiles-graph/src/test/java/nl/tudelft/lifetiles/graph/view/TileViewTest.java

@@ -16,9 +16,11 @@
 import javafx.scene.input.MouseButton;
 import javafx.scene.input.MouseEvent;
 import javafx.scene.shape.Rectangle;
+import javafx.scene.shape.Circle;
 import nl.tudelft.lifetiles.annotation.model.KnownMutation;
 import nl.tudelft.lifetiles.annotation.model.KnownMutationMapper;
 import nl.tudelft.lifetiles.annotation.model.KnownMutationParser;
+import nl.tudelft.lifetiles.core.util.Settings;
 import nl.tudelft.lifetiles.graph.controller.GraphController;
 import nl.tudelft.lifetiles.graph.model.BucketCache;
 import nl.tudelft.lifetiles.graph.model.FactoryProducer;
@@ -107,7 +109,7 @@ public void drawVerticeTest() {
 
     }
 
-    private Rectangle rec;
+    private Circle bookmark;
     private VertexView vView1;
 
     @Test
@@ -148,7 +150,7 @@ public void drawAnnotationTest() throws IOException, InterruptedException {
             Group result = tileview.drawGraph(buckets.getSegments(0, 1), graph,
                     annotations, 1);
 
-            rec = (Rectangle) ((Group) result.getChildrenUnmodifiable().get(2))
+            bookmark = (Circle) ((Group) result.getChildrenUnmodifiable().get(2))
                     .getChildrenUnmodifiable().get(0);
 
             vView1 = (VertexView) ((Group) result.getChildrenUnmodifiable()
@@ -157,7 +159,7 @@ public void drawAnnotationTest() throws IOException, InterruptedException {
         });
 
         Thread.sleep(1000);
-        assertEquals(rec.getHeight(), vView1.getHeight(), 1e-10);
+        assertEquals(bookmark.getRadius(), Double.parseDouble(Settings.get("bookmark_radius")), 1e-10);
     }
 
     @Test