X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=d15a6e807b1406e4927f50aaa885f2ccf924cadf;hb=44d9bd9b511490baec5302be3b7756be0adebde3;hp=af6e2554703b141d87316e08c541167fb7ee3b58;hpb=c7b0119ea09d3650762275bd96e2d5e61161aa8d;p=jalview.git

diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index af6e255..d15a6e8 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -50,22 +50,41 @@ public class HTMLOutput
 
 
         //////////////
-        SequenceGroup group;
+        SequenceGroup [] groups;
         SequenceI seq;
-        ColourSchemeI cs;
+        ColourSchemeI cs = null;
         AlignmentI alignment = av.getAlignment();
         String r,g,b;
-        for (int i = 0; i < alignment.getHeight(); i++)
+
+      // draws the top row, the measure rule
+        out.println("<tr><td colspan=\"6\"></td>");
+        int i=0;
+        for(i=10; i<alignment.getWidth()-10; i+=10)
+          out.println("<td colspan=\"9\">"+i+"<br>|</td><td></td>");
+
+        out.println("<td colspan=\"3\"></td><td colspan=\"3\">"+i+"<br>|</td>");
+        out.println("</tr>");
+
+        for (i = 0; i < alignment.getHeight(); i++)
         {
           seq = alignment.getSequenceAt(i);
-          group = alignment.findGroup( seq );
+          groups = alignment.findAllGroups( seq );
           out.println("<tr><td nowrap>"+seq.getDisplayId()+"&nbsp;&nbsp;</td>");
+
+
           for (int res = 0; res < seq.getLength(); res++)
           {
-            if(group!=null && group.getStartRes()<=res && group.getEndRes()>=res)
-              cs = group.cs;
-            else
-              cs = av.getGlobalColourScheme();
+            cs = av.getGlobalColourScheme();
+
+            if(groups!=null)
+             {
+               for (int k = 0; k < groups.length; k++)
+                 if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)
+                 {
+                   cs = groups[k].cs;
+                   break;
+                 }
+             }
 
 
             color = sr.getResidueBoxColour(cs, seq, res);