JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...

[jalview.git] / src / jalview / analysis / AAFrequency.java

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index d56fb01..58531de 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -44,20 +44,21 @@ public class AAFrequency
 
   public static final String PROFILE = "P";
 
-  public static final Hashtable[] calculate(Vector sequences, int start,
+  public static final Hashtable[] calculate(List<SequenceI> list, int start,
           int end)
   {
-    return calculate(sequences, start, end, false);
+    return calculate(list, start, end, false);
   }
 
-  public static final Hashtable[] calculate(Vector sequences, int start,
+  public static final Hashtable[] calculate(List<SequenceI> sequences, int start,
           int end, boolean profile)
   {
     SequenceI[] seqs = new SequenceI[sequences.size()];
     int width = 0;
+    synchronized (sequences) {
     for (int i = 0; i < sequences.size(); i++)
     {
-      seqs[i] = (SequenceI) sequences.elementAt(i);
+      seqs[i] = sequences.get(i);
       if (seqs[i].getLength() > width)
       {
         width = seqs[i].getLength();
@@ -72,9 +73,9 @@ public class AAFrequency
     }
 
     calculate(seqs, start, end, reply, profile);
-
     return reply;
   }
+  }
 
   public static final void calculate(SequenceI[] sequences, int start,
           int end, Hashtable[] result)