JAL-2527 Updates following code review

[jalview.git] / src / jalview / renderer / OverviewResColourFinder.java

diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java
index 07fc6e3..b606ba3 100644 (file)
--- a/src/jalview/renderer/OverviewResColourFinder.java
+++ b/src/jalview/renderer/OverviewResColourFinder.java
@@ -22,6 +22,7 @@ package jalview.renderer;
 
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Preferences;
 import jalview.util.Comparison;
 
 import java.awt.Color;
@@ -41,9 +42,8 @@ public class OverviewResColourFinder extends ResidueColourFinder
    */
   public OverviewResColourFinder()
   {
-    GAP_COLOUR = Color.lightGray;
-    RESIDUE_COLOUR = Color.white;
-    HIDDEN_COLOUR = Color.DARK_GRAY.darker();
+    this(false, Preferences.OVERVIEW_DEFAULT_GAP,
+            Preferences.OVERVIEW_DEFAULT_HIDDEN);
   }
 
   /**
@@ -84,8 +84,8 @@ public class OverviewResColourFinder extends ResidueColourFinder
     // settings
     if (shader.getColourScheme() != null)
     {
-      if (!shader.getColourScheme().hasGapColour()
-              && Comparison.isGap(currentChar))
+      if (Comparison.isGap(currentChar)
+              && (!shader.getColourScheme().hasGapColour()))
       {
         resBoxColour = GAP_COLOUR;
       }