applet can define groups as parameters

[jalview.git] / src / jalview / io / AnnotationFile.java

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