X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=8ec234d12128745ff90f873ed3fa50611d9448c0;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=56040d9059083908a6063cddcb9ae66f6237b132;hpb=6a44f113099e7ee83deada4d8426cd98757c2425;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 56040d9..8ec234d 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -225,7 +225,6 @@ public class AnnotationFile
 
 
   SequenceI refSeq = null;
-  Hashtable annotationsHash = new Hashtable();
   public boolean readAnnotationFile(AlignmentI al,
                                     String file,
                                     String protocol)
@@ -591,7 +590,6 @@ public class AnnotationFile
     if(sg.getSize()>0)
     {
       al.addGroup(sg);
-      annotationsHash.put(sg.getName(), sg);
     }
   }
 
@@ -601,7 +599,21 @@ public class AnnotationFile
     //So far we have only added groups to the annotationHash,
     //the idea is in the future properties can be added to
     //alignments, other annotations etc
-    SequenceGroup sg = (SequenceGroup)annotationsHash.get(st.nextToken());
+    if(al.getGroups()==null)
+      return;
+    SequenceGroup sg = null;
+
+    String name = st.nextToken();
+
+    Vector groups = al.getGroups();
+    for(int i=0; i<groups.size(); i++)
+    {
+      sg = (SequenceGroup)groups.elementAt(i);
+      if(sg.getName().equals(name))
+        break;
+      else
+        sg = null;
+    }
 
     if(sg!=null)
     {