Correction for feature rendering

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