X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=b3b2111540fecc0a369da12f8d9dce01630bf5d1;hb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;hp=d4284a24e8612682f3b7492c856a3bc332c5f8e6;hpb=e601d78bc7762386f570e346a803684c43a66ff1;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index d4284a2..b3b2111 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -68,14 +68,14 @@ public class AnnotationFile
    * columns or hidden row keywords.
    * 
    * @param annotations
-   * @param groups
+   * @param list
    * @param properties
    * @return feature file as a string.
    */
   public String printAnnotations(AlignmentAnnotation[] annotations,
-          Vector groups, Hashtable properties)
+          List<SequenceGroup> list, Hashtable properties)
   {
-    return printAnnotations(annotations, groups, properties, null);
+    return printAnnotations(annotations, list, properties, null);
 
   }
 
@@ -110,13 +110,13 @@ public class AnnotationFile
    * properties and views.
    * 
    * @param annotations
-   * @param groups
+   * @param list
    * @param properties
    * @param views
    * @return annotation file
    */
   public String printAnnotations(AlignmentAnnotation[] annotations,
-          Vector groups, Hashtable properties, ViewDef[] views)
+          List<SequenceGroup> list, Hashtable properties, ViewDef[] views)
   {
     // TODO: resolve views issue : annotationFile could contain visible region,
     // or full data + hidden region specifications for a view.
@@ -393,9 +393,9 @@ public class AnnotationFile
       text.append(rowprops.toString());
     }
 
-    if (groups != null)
+    if (list != null)
     {
-      printGroups(groups);
+      printGroups(list);
     }
 
     if (properties != null)
@@ -419,13 +419,11 @@ public class AnnotationFile
     return text.toString();
   }
 
-  public void printGroups(Vector sequenceGroups)
+  public void printGroups(List<SequenceGroup> list)
   {
-    SequenceGroup sg;
     SequenceI seqrep = null;
-    for (int i = 0; i < sequenceGroups.size(); i++)
+    for (SequenceGroup sg:list)
     {
-      sg = (SequenceGroup) sequenceGroups.elementAt(i);
       if (!sg.hasSeqrep())
       {
         text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
@@ -889,17 +887,14 @@ public class AnnotationFile
       }
       // Finally, resolve the groupRefs
       Enumeration en = groupRefRows.keys();
-      SequenceGroup theGroup = null;
-
+      
       while (en.hasMoreElements())
       {
         groupRef = (String) en.nextElement();
         boolean matched = false;
         // Resolve group: TODO: add a getGroupByName method to alignments
-        Vector grps = al.getGroups();
-        for (int g = 0, gSize = grps.size(); g < gSize; g++)
+        for (SequenceGroup theGroup : al.getGroups())
         {
-          theGroup = (SequenceGroup) grps.elementAt(g);
           if (theGroup.getName().equals(groupRef))
           {
             if (matched)
@@ -1018,7 +1013,7 @@ public class AnnotationFile
         }
       }
       if (hasSymbols
-              && (token.equals("H") || token.equals("E") || token
+              && (token.equals("H") || token.equals("E") || token.equals("S") || token
                       .equals(" ")))
       {
         // Either this character represents a helix or sheet
@@ -1293,15 +1288,12 @@ public class AnnotationFile
     {
       return;
     }
-    SequenceGroup sg = null;
-
+    
     String name = st.nextToken();
-
-    Vector groups = al.getGroups();
-    for (int i = 0; i < groups.size(); i++)
+    SequenceGroup sg=null;
+    for (SequenceGroup _sg:al.getGroups())
     {
-      sg = (SequenceGroup) groups.elementAt(i);
-      if (sg.getName().equals(name))
+      if ((sg=_sg).getName().equals(name))
       {
         break;
       }
@@ -1343,7 +1335,7 @@ public class AnnotationFile
                   sg.getStartRes(), sg.getEndRes() + 1);
 
           c.calculate();
-          c.verdict(false, 25);
+          c.verdict(false, 25); // TODO: refer to conservation percent threshold
 
           sg.cs.setConservation(c);