JAL-2527 Updates following code review

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

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 63075dc..ed1497a 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.bin.Cache;
 import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
@@ -57,6 +59,8 @@ public class OverviewCanvas extends JComponent
 
   private AlignViewportI av;
 
+  private OverviewResColourFinder cf;
+
   public OverviewCanvas(OverviewDimensions overviewDims,
           AlignViewportI alignvp)
   {
@@ -65,8 +69,14 @@ 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,
+            Preferences.OVERVIEW_DEFAULT_GAP);
+    Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
+            Preferences.OVERVIEW_DEFAULT_HIDDEN);
+    cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
   }
 
   /**
@@ -119,29 +129,17 @@ public class OverviewCanvas extends JComponent
   {
     miniMe = null;
 
-    if (!av.getShowBoxes())
+    if (showSequenceFeatures)
     {
-      // boxes are not shown on main viewport
-      or = new OverviewRenderer(sr, fr, od);
-      miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
-              BufferedImage.TYPE_INT_RGB);
-      miniMe.getGraphics().setColor(Color.WHITE);
-      miniMe.getGraphics().fillRect(0, 0, od.getWidth(),
-              od.getSequencesHeight());
+      fr.transferSettings(transferRenderer);
     }
-    else
-    {
-      if (showSequenceFeatures)
-      {
-        fr.transferSettings(transferRenderer);
-      }
 
-      setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
+    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
-      or = new OverviewRenderer(sr, fr, od);
-      miniMe = or.draw(od.getRows(av.getAlignment()),
-              od.getColumns(av.getAlignment()));
-    }
+    or = new OverviewRenderer(fr, od, av.getAlignment(),
+            av.getResidueShading(), cf);
+    miniMe = or.draw(od.getRows(av.getAlignment()),
+            od.getColumns(av.getAlignment()));
 
     Graphics mg = miniMe.getGraphics();