JAL-845 linked protein/dna 'slave' further PoC functionality

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 752c6d4..9c046c6 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -27,7 +27,6 @@ import jalview.schemes.ResidueProperties;
 
 import java.awt.Color;
 import java.util.ArrayList;
-import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -160,13 +159,10 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     if (seqsel != null)
     {
-      sequences = new Vector();
-      Enumeration<SequenceI> sq = seqsel.sequences.elements();
-      while (sq.hasMoreElements())
+      for (SequenceI seq : seqsel.sequences)
       {
-        sequences.addElement(sq.nextElement());
+        sequences.addElement(seq);
       }
-      ;
       if (seqsel.groupName != null)
       {
         groupName = new String(seqsel.groupName);
@@ -989,12 +985,15 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     SequenceGroup sgroup = new SequenceGroup(this);
     SequenceI[] insect = getSequencesInOrder(alignment);
-    sgroup.sequences = new Vector();
-    for (int s = 0; insect != null && s < insect.length; s++)
+    sgroup.sequences = new Vector<SequenceI>();
+    if (insect != null)
     {
-      if (map == null || map.containsKey(insect[s]))
+      for (SequenceI seq : insect)
       {
-        sgroup.sequences.addElement(insect[s]);
+        if (map == null || map.containsKey(seq))
+        {
+          sgroup.sequences.addElement(seq);
+        }
       }
     }
     // Enumeration en =getSequences(hashtable).elements();