X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=3104772f712b409efc20e9a6a8ad00cdc0915801;hb=c0501eaa85c0594f9275766f64de8ea44a59c368;hp=3202ac9f8b067fddcbf26f82e52811390f9fcdf9;hpb=04c8f7bff663aa469127e9eed4164e02933782f1;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 3202ac9..3104772 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -341,9 +341,9 @@ public abstract class AlignFile extends FileParse
    */
   protected void initData()
   {
-    seqs = new Vector<SequenceI>();
-    annotations = new Vector<AlignmentAnnotation>();
-    seqGroups = new ArrayList<SequenceGroup>();
+    seqs = new Vector<>();
+    annotations = new Vector<>();
+    seqGroups = new ArrayList<>();
     parseCalled = false;
   }
 
@@ -356,7 +356,7 @@ public abstract class AlignFile extends FileParse
   @Override
   public void setSeqs(SequenceI[] s)
   {
-    seqs = new Vector<SequenceI>();
+    seqs = new Vector<>();
 
     for (int i = 0; i < s.length; i++)
     {
@@ -427,7 +427,7 @@ public abstract class AlignFile extends FileParse
   {
     if (newickStrings == null)
     {
-      newickStrings = new Vector<String[]>();
+      newickStrings = new Vector<>();
     }
     newickStrings.addElement(new String[] { treeName, newickString });
   }
@@ -451,4 +451,16 @@ public abstract class AlignFile extends FileParse
   {
     seqs.add(seq);
   }
+
+  /**
+   * Used only for hmmer statistics, so should probably be removed at some
+   * point. TODO remove this
+   * 
+   * @return
+   */
+  public Vector<AlignmentAnnotation> getAnnotations()
+  {
+    return annotations;
+  }
+
 }