From 21559d1d8350538846655bfa6ccfc7320dd9e2e5 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 9 Dec 2010 17:34:45 +0000
Subject: [PATCH] fix case when groups overlap - ensure groups are non-empty
 and always add up to length of alignment

---
 src/jalview/ws/rest/params/SeqGroupIndexVector.java |    8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/jalview/ws/rest/params/SeqGroupIndexVector.java b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
index 66724b8..1a7c63f 100644
--- a/src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@ -80,14 +80,18 @@ public class SeqGroupIndexVector extends InputType implements AlignmentProcessor
       srt[i]=vals[i][0];
     jalview.util.QuickSort.sort(srt, vals);
     list=false;
+    int last=vals[0][0];
     for (int[] range:vals)
     {
-      if (list)
+      if (range[1]>last) {
+        if (list)
       {
         idvector.append(sep);
       }
-      idvector.append(range[1]-range[0]+1);
+      idvector.append(range[1]-last+1);
+      last=range[1];
       list=true;
+      }
     }
     return new StringBody(idvector.toString());
   }
-- 
1.7.10.2