JAL-2527 Wired up cached values to overview

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

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 90181f8..3ea5e9b 100644 (file)
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -21,7 +21,9 @@
 package jalview.gui;
 
 import jalview.api.AlignViewportI;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.bin.Cache;
+import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
@@ -53,6 +55,8 @@ public class OverviewCanvas extends JComponent
 
   private OverviewDimensions od;
 
+  private OverviewRenderer or = null;
+
   private AlignViewportI av;
 
   public OverviewCanvas(OverviewDimensions overviewDims,
@@ -63,7 +67,6 @@ public class OverviewCanvas extends JComponent
 
     sr = new SequenceRenderer(av);
     sr.renderGaps = false;
-    sr.forOverview = true;
     fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
   }
 
@@ -89,6 +92,10 @@ public class OverviewCanvas extends JComponent
       if (updaterunning)
       {
         restart = true;
+        if (or != null)
+        {
+          or.setRedraw(true);
+        }
       }
       else
       {
@@ -117,15 +124,18 @@ public class OverviewCanvas extends JComponent
     {
       fr.transferSettings(transferRenderer);
     }
-    FeatureColourFinder finder = new FeatureColourFinder(fr);
 
-    // why do we need to set preferred size again? was set in
-    // updateOverviewImage
     setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
-    OverviewRenderer or = new OverviewRenderer(sr, finder, od);
+    boolean useLegacy = Cache.getDefault("USE_LEGACY_GAP", false);
+    Color gapCol = Cache.getDefaultColour("GAP_COLOUR", new Color(240, 240, 240));
+    Color hiddenCol = Cache.getDefaultColour("HIDDEN_COLOUR", Color.DARK_GRAY.darker());
+    OverviewResColourFinder cf = new OverviewResColourFinder(useLegacy,
+            gapCol, hiddenCol);
+    or = new OverviewRenderer(fr, od, av.getAlignment(),
+            av.getResidueShading(), cf);
     miniMe = or.draw(od.getRows(av.getAlignment()),
-            od.getColumns(av.getAlignment().getHiddenColumns()));
+            od.getColumns(av.getAlignment()));
 
     Graphics mg = miniMe.getGraphics();
 
@@ -134,7 +144,7 @@ public class OverviewCanvas extends JComponent
       mg.translate(0, od.getSequencesHeight());
       or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
               av.getCharWidth(), od.getGraphHeight(),
-              od.getColumns(av.getAlignment().getHiddenColumns()));
+              od.getColumns(av.getAlignment()));
       mg.translate(0, -od.getSequencesHeight());
     }
     System.gc();