From c4d90a3a0491fd14fdf03987486f50471636ebce Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 28 Nov 2005 17:15:06 +0000
Subject: [PATCH] Correction for feature rendering

---
 src/jalview/io/HTMLOutput.java |   19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 00c7364..beb8829 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -24,7 +24,6 @@ import java.awt.*;
 
 import jalview.datamodel.*;
 import jalview.gui.*;
-import jalview.schemes.*;
 
 public class HTMLOutput
 {
@@ -141,10 +140,15 @@ public class HTMLOutput
 
       for (int res = 0; res < seq.getLength(); res++)
       {
+        if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+        {
+          color = sr.getResidueBoxColour(seq, res);
 
-        color = sr.findSequenceColour(Color.white, seq, res);
+          color = fr.findFeatureColour(color, seq, res);
+        }
+        else
+            color = Color.white;
 
-        color = fr.findFeatureColour(color, seq, res);
 
        if (color.getRGB() < -1)
         {
@@ -235,9 +239,14 @@ public class HTMLOutput
 
         for (int res = startRes; res < endRes; res++)
         {
-          color = sr.findSequenceColour(Color.white, seq, res);
+          if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+          {
+            color = sr.getResidueBoxColour(seq, res);
 
-          color = fr.findFeatureColour(color, seq, res);
+            color = fr.findFeatureColour(color, seq, res);
+          }
+          else
+            color = Color.white;
 
           if (color.getRGB() < -1)
           {
-- 
1.7.10.2