X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=5778a7e4ae06dd61df596339b12284dac70bdb14;hb=cc6f7ebe59c148e62cd9f1947d9ba30638db2980;hp=3319b338db89f9b4e00ac3e7aa9b76941c884733;hpb=df1c58f9669c477db082016aa919d6c6cc9da071;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3319b33..5778a7e 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2586,8 +2586,6 @@ public boolean parseGroupsFile(String file)
           end = Integer.parseInt(st.nextToken());
 
           seq = viewport.alignment.getSequenceAt(index);
-          start = seq.findIndex(start) - 1;
-          end = seq.findIndex(end) - 1;
 
           type = st.nextToken();
 
@@ -2606,6 +2604,7 @@ public boolean parseGroupsFile(String file)
     }
     catch (Exception ex)
     {
+      ex.printStackTrace();
       System.out.println("Error parsing groups file: " + ex);
       return false;
     }