From 96f41aa46d3e568f8734834ab36fdc9ad8e54ac1 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 5 Apr 2010 15:38:53 +0000
Subject: [PATCH] javadoc, and unimplemented warning for group associated
 annotation (not shared to vamsas session in 2.5)

---
 src/jalview/io/VamsasAppDatastore.java |   10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index a9219a6..e313470 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -58,7 +58,9 @@ import uk.ac.vamsas.objects.utils.Properties;
  * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
  * 
  */
-
+/*
+ * TODO: check/verify consistency for vamsas sync with group associated alignment annotation  
+ */
 public class VamsasAppDatastore
 {
   /**
@@ -516,6 +518,12 @@ public class VamsasAppDatastore
           {
             continue;
           }
+          if (aa[i].groupRef!=null)
+          {
+            // TODO: store any group associated annotation references
+            Cache.log.warn("Group associated sequence annotation is not stored in VAMSAS document.");
+            continue;
+          }
           if (aa[i].sequenceRef != null)
           {
             // Deal with sequence associated annotation
-- 
1.7.10.2