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

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

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 8e596ce..a23aad5 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -21,6 +21,7 @@ import jalview.util.ShiftList;
 \r
 import java.io.PrintStream;\r
 import java.util.Enumeration;\r
+import java.util.List;\r
 import java.util.Vector;\r
 \r
 /**\r
@@ -105,7 +106,7 @@ public class AlignmentView
     SequenceI[] selseqs;\r
     if (selection != null)\r
     {\r
-      Vector sel = selection.getSequences(null);\r
+      List<SequenceI> sel = selection.getSequences(null);\r
       this.selected = new Vector();\r
       selseqs = selection.getSequencesInOrder(alignment, selectedRegionOnly);\r
     }\r
@@ -116,12 +117,8 @@ public class AlignmentView
 \r
     // get the alignment's group list and make a copy\r
     Vector grps = new Vector();\r
-    Vector gg = alignment.getGroups();\r
-    Enumeration gge = gg.elements();\r
-    while (gge.hasMoreElements())\r
-    {\r
-      grps.addElement(gge.nextElement());\r
-    }\r
+    List<SequenceGroup> gg = alignment.getGroups();\r
+    grps.addAll(gg);\r
     ScGroup[] sgrps = null;\r
     boolean addedgps[] = null;\r
     if (grps != null)\r
@@ -1047,12 +1044,10 @@ public class AlignmentView
                 + " wide and has " + visal.getHeight() + " seqs.");\r
         if (visal.getGroups() != null && visal.getGroups().size() > 0)\r
         {\r
-          SequenceGroup sg;\r
-          Enumeration en = visal.getGroups().elements();\r
+          \r
           int i = 1;\r
-          while (en.hasMoreElements())\r
+          for (SequenceGroup sg:visal.getGroups())\r
           {\r
-            sg = (SequenceGroup) en.nextElement();\r
             os.println("Group " + (i++) + " begins at column "\r
                     + sg.getStartRes() + " and ends at " + sg.getEndRes());\r
           }\r