added description of alignment quality scores and separated

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

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 889df36..0fa8b2e 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -33,6 +33,7 @@ public class SequenceRenderer
   SequenceGroup[] allGroups = null;\r
   Color resBoxColour;\r
   Graphics graphics;\r
+  boolean forOverview = false;\r
 \r
   public SequenceRenderer(AlignViewport av)\r
   {\r
@@ -69,10 +70,15 @@ public class SequenceRenderer
     {\r
       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);\r
     }\r
+    else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))\r
+    {\r
+        resBoxColour = Color.lightGray;\r
+    }\r
     else\r
     {\r
       resBoxColour = Color.white;\r
     }\r
+\r
   }\r
 \r
   public Color findSequenceColour(SequenceI seq, int i)\r