From: kiramt <k.mourao@dundee.ac.uk>
Date: Mon, 5 Jun 2017 19:45:06 +0000 (+0100)
Subject: JAL-2588 Naive implementation of gaps as grey in overview
X-Git-Tag: Release_2_10_3b1~142^2~2^2~9^2~3^2~9
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7d722306ebba9a2d6562849c598a91d867f7d00e;p=jalview.git

JAL-2588 Naive implementation of gaps as grey in overview
---

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 36825ea..a89d7ce 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -140,8 +140,15 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   {
     if (shader.getColourScheme() != null)
     {
-      resBoxColour = shader.findColour(seq.getCharAt(i),
+      if (forOverview && Comparison.isGap(seq.getCharAt(i)))
+      {
+        resBoxColour = Color.lightGray;
+      }
+      else
+      {
+        resBoxColour = shader.findColour(seq.getCharAt(i),
               i, seq);
+      }
     }
     else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
     {