JAL-2629 update spikes/mungo to latest

[jalview.git] / src / jalview / appletgui / OverviewCanvas.java

diff --git a/src/jalview/appletgui/OverviewCanvas.java b/src/jalview/appletgui/OverviewCanvas.java
index ede3b94..e99c021 100644 (file)
--- a/src/jalview/appletgui/OverviewCanvas.java
+++ b/src/jalview/appletgui/OverviewCanvas.java
@@ -21,17 +21,17 @@
 package jalview.appletgui;
 
 import jalview.renderer.OverviewRenderer;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.renderer.OverviewResColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
+import java.awt.Component;
 import java.awt.Dimension;
 import java.awt.Frame;
 import java.awt.Graphics;
 import java.awt.Image;
-import java.awt.Panel;
 
-public class OverviewCanvas extends Panel
+public class OverviewCanvas extends Component
 {
   // This is set true if the alignment view changes whilst
   // the overview is being calculated
@@ -41,16 +41,14 @@ public class OverviewCanvas extends Panel
 
   private OverviewDimensions od;
 
+  private OverviewRenderer or = null;
+
   private Image miniMe;
 
   private Image offscreen;
 
   private AlignViewport av;
 
-  // Can set different properties in this seqCanvas than
-  // main visible SeqCanvas
-  private SequenceRenderer sr;
-
   private jalview.renderer.seqfeatures.FeatureRenderer fr;
 
   private Frame nullFrame;
@@ -64,10 +62,6 @@ public class OverviewCanvas extends Panel
     nullFrame = new Frame();
     nullFrame.addNotify();
 
-    sr = new SequenceRenderer(av);
-    sr.graphics = nullFrame.getGraphics();
-    sr.renderGaps = false;
-    sr.forOverview = true;
     fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
   }
 
@@ -93,6 +87,10 @@ public class OverviewCanvas extends Panel
       if (updaterunning)
       {
         restart = true;
+        if (or != null)
+        {
+          or.setRedraw(true);
+        }
       }
       else
       {
@@ -102,16 +100,6 @@ public class OverviewCanvas extends Panel
     }
   }
 
-  /**
-   * Draw the overview sequences
-   * 
-   * @param showSequenceFeatures
-   *          true if sequence features are to be shown
-   * @param showAnnotation
-   *          true if the annotation is to be shown
-   * @param transferRenderer
-   *          the renderer to transfer feature colouring from
-   */
   public void draw(boolean showSequenceFeatures, boolean showAnnotation,
           FeatureRenderer transferRenderer)
   {
@@ -121,16 +109,16 @@ public class OverviewCanvas extends Panel
     {
       fr.transferSettings(transferRenderer);
     }
-    FeatureColourFinder finder = new FeatureColourFinder(fr);
 
     setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
-    OverviewRenderer or = new OverviewRenderer(sr, finder, od);
+    or = new OverviewRenderer(fr, od, av.getAlignment(),
+            av.getResidueShading(), new OverviewResColourFinder());
     miniMe = nullFrame.createImage(od.getWidth(), od.getHeight());
     offscreen = nullFrame.createImage(od.getWidth(), od.getHeight());
 
     miniMe = or.draw(od.getRows(av.getAlignment()),
-            od.getColumns(av.getAlignment().getHiddenColumns()));
+            od.getColumns(av.getAlignment()));
 
     Graphics mg = miniMe.getGraphics();
 
@@ -140,11 +128,9 @@ public class OverviewCanvas extends Panel
     {
       mg.translate(0, od.getSequencesHeight());
       or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
-              av.getCharWidth(), od.getGraphHeight(),
-              od.getColumns(av.getAlignment().getHiddenColumns()));
+              od.getGraphHeight(), od.getColumns(av.getAlignment()));
       mg.translate(0, -od.getSequencesHeight());
     }
-    System.gc();
 
     if (restart)
     {