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

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

diff --git a/src/jalview/analysis/Grouping.java b/src/jalview/analysis/Grouping.java
index 95323e6..91fef84 100644 (file)
--- a/src/jalview/analysis/Grouping.java
+++ b/src/jalview/analysis/Grouping.java
@@ -24,6 +24,7 @@ import jalview.datamodel.SequenceI;
 
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 /**
@@ -42,25 +43,24 @@ public class Grouping
    * 
    * @param sequences
    * @param selectedChars
-   * @param exgroups
+   * @param list
    * @return
    */
   public static SequenceGroup[] makeGroupsFrom(SequenceI[] sequences,
-          String[] selectedChars, Vector exgroups)
+          String[] selectedChars, List<SequenceGroup> list)
   {
     // TODO: determine how to get/recover input data for group generation
     Hashtable gps = new Hashtable();
     int width = 0, i;
     Hashtable pgroup = new Hashtable();
-    if (exgroups != null)
+    if (list != null)
     {
-      SequenceGroup sg;
-      for (Enumeration g = exgroups.elements(); g.hasMoreElements();)
+      for (SequenceGroup sg:list)
       {
-        sg = (SequenceGroup) g.nextElement();
-        for (Enumeration sq = sg.getSequences(null).elements(); sq
-                .hasMoreElements();)
-          pgroup.put(sq.nextElement().toString(), sg);
+        for (SequenceI sq :sg.getSequences(null))
+        {
+          pgroup.put(sq.toString(), sg);
+        }
       }
     }
     for (i = 0; i < sequences.length; i++)