X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewCanvas.java;h=9df0d82eaa472e400433e1b1fdb4c16ff4df7e3c;hb=d7e95f458ebcbbdcc13f8b07357542ab2d7e4547;hp=daa602d6b6bc50654a9efdc33dbd27e4c274ed19;hpb=2d137c4d89286572fba9e1f81eee9b35e4ca4a97;p=jalview.git

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index daa602d..9df0d82 100644
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -21,10 +21,13 @@
 package jalview.gui;
 
 import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
 import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
+import java.awt.Dimension;
 import java.awt.Graphics;
 import java.awt.image.BufferedImage;
 
@@ -58,6 +61,8 @@ public class OverviewCanvas extends JComponent
 
   private AlignViewportI av;
 
+  private OverviewResColourFinder cf;
+
   private ProgressPanel progressPanel;
 
   public OverviewCanvas(OverviewDimensions overviewDims,
@@ -69,9 +74,15 @@ public class OverviewCanvas extends JComponent
 
     sr = new SequenceRenderer(av);
     sr.renderGaps = false;
-    sr.forOverview = true;
     fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
 
+    boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
+    Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+    Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
+    cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
+
     setSize(od.getWidth(), od.getHeight());
   }
 
@@ -130,8 +141,13 @@ public class OverviewCanvas extends JComponent
       fr.transferSettings(transferRenderer);
     }
 
-    or = new OverviewRenderer(sr, fr, od);
+    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
+
+    or = new OverviewRenderer(fr, od, av.getAlignment(),
+            av.getResidueShading(), cf);
+
     or.addPropertyChangeListener(progressPanel);
+
     miniMe = or.draw(od.getRows(av.getAlignment()),
             od.getColumns(av.getAlignment()));
 
@@ -167,6 +183,8 @@ public class OverviewCanvas extends JComponent
   @Override
   public void paintComponent(Graphics g)
   {
+    super.paintComponent(g);
+
     if (restart)
     {
       if (lastMiniMe == null)
@@ -188,7 +206,8 @@ public class OverviewCanvas extends JComponent
               && ((getWidth() != od.getWidth())
                       || (getHeight() != od.getHeight())))
       {
-        // if there is annotation, scale the alignment and annotation separately
+        // if there is annotation, scale the alignment and annotation
+        // separately
         if (od.getGraphHeight() > 0)
         {
           BufferedImage topImage = lastMiniMe.getSubimage(0, 0,
@@ -219,25 +238,24 @@ public class OverviewCanvas extends JComponent
           od.setHeight(getHeight());
         }
 
-        // scale lastMiniMe to the new size
-        g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
-
         // make sure the box is in the right place
         od.setBoxPosition(av.getAlignment().getHiddenSequences(),
                 av.getAlignment().getHiddenColumns());
       }
-      else // not a resize
-      {
-        // fall back to normal behaviour
-        g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
-      }
+      // fall back to normal behaviour
+      g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
     }
-
+    else
+    {
+      g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+    }
+    
     // draw the box
     g.setColor(Color.red);
     od.drawBox(g);
   }
 
+
   public void dispose()
   {
     dispose = true;