JAL-1421 changed Vector to List<String> for protein-to-codon mappings

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index c11423c..6cea8f0 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -633,47 +633,47 @@ public class ResidueProperties
   public static final float[] pidThresholds =
   { 80, 60, 40, };
 
-  public static Hashtable codonHash = new Hashtable();
+  public static Map<String, List<String>> codonHash = new HashMap<String, List<String>>();
 
-  public static Vector Lys = new Vector();
+  private static List<String> Lys = new ArrayList<String>();
 
-  public static Vector Asn = new Vector();
+  private static List<String> Asn = new ArrayList<String>();
 
-  public static Vector Gln = new Vector();
+  private static List<String> Gln = new ArrayList<String>();
 
-  public static Vector His = new Vector();
+  private static List<String> His = new ArrayList<String>();
 
-  public static Vector Glu = new Vector();
+  private static List<String> Glu = new ArrayList<String>();
 
-  public static Vector Asp = new Vector();
+  private static List<String> Asp = new ArrayList<String>();
 
-  public static Vector Tyr = new Vector();
+  private static List<String> Tyr = new ArrayList<String>();
 
-  public static Vector Thr = new Vector();
+  private static List<String> Thr = new ArrayList<String>();
 
-  public static Vector Pro = new Vector();
+  private static List<String> Pro = new ArrayList<String>();
 
-  public static Vector Ala = new Vector();
+  private static List<String> Ala = new ArrayList<String>();
 
-  public static Vector Ser = new Vector();
+  private static List<String> Ser = new ArrayList<String>();
 
-  public static Vector Arg = new Vector();
+  private static List<String> Arg = new ArrayList<String>();
 
-  public static Vector Gly = new Vector();
+  private static List<String> Gly = new ArrayList<String>();
 
-  public static Vector Trp = new Vector();
+  private static List<String> Trp = new ArrayList<String>();
 
-  public static Vector Cys = new Vector();
+  private static List<String> Cys = new ArrayList<String>();
 
-  public static Vector Ile = new Vector();
+  private static List<String> Ile = new ArrayList<String>();
 
-  public static Vector Met = new Vector();
+  private static List<String> Met = new ArrayList<String>();
 
-  public static Vector Leu = new Vector();
+  private static List<String> Leu = new ArrayList<String>();
 
-  public static Vector Val = new Vector();
+  private static List<String> Val = new ArrayList<String>();
 
-  public static Vector Phe = new Vector();
+  private static List<String> Phe = new ArrayList<String>();
 
   public static List<String> STOP = new ArrayList<String>();
 
@@ -1047,87 +1047,87 @@ public class ResidueProperties
 
   static
   {
-    Lys.addElement("AAA");
-    Lys.addElement("AAG");
-    Asn.addElement("AAC");
-    Asn.addElement("AAT");
-
-    Gln.addElement("CAA");
-    Gln.addElement("CAG");
-    His.addElement("CAC");
-    His.addElement("CAT");
-
-    Glu.addElement("GAA");
-    Glu.addElement("GAG");
-    Asp.addElement("GAC");
-    Asp.addElement("GAT");
-
-    Tyr.addElement("TAC");
-    Tyr.addElement("TAT");
-
-    Thr.addElement("ACA");
-    Thr.addElement("ACG");
-    Thr.addElement("ACC");
-    Thr.addElement("ACT");
-
-    Pro.addElement("CCA");
-    Pro.addElement("CCG");
-    Pro.addElement("CCC");
-    Pro.addElement("CCT");
-
-    Ala.addElement("GCA");
-    Ala.addElement("GCG");
-    Ala.addElement("GCC");
-    Ala.addElement("GCT");
-
-    Ser.addElement("TCA");
-    Ser.addElement("TCG");
-    Ser.addElement("TCC");
-    Ser.addElement("TCT");
-    Ser.addElement("AGC");
-    Ser.addElement("AGT");
-
-    Arg.addElement("AGA");
-    Arg.addElement("AGG");
-    Arg.addElement("CGA");
-    Arg.addElement("CGG");
-    Arg.addElement("CGC");
-    Arg.addElement("CGT");
-
-    Gly.addElement("GGA");
-    Gly.addElement("GGG");
-    Gly.addElement("GGC");
-    Gly.addElement("GGT");
+    Lys.add("AAA");
+    Lys.add("AAG");
+    Asn.add("AAC");
+    Asn.add("AAT");
+
+    Gln.add("CAA");
+    Gln.add("CAG");
+    His.add("CAC");
+    His.add("CAT");
+
+    Glu.add("GAA");
+    Glu.add("GAG");
+    Asp.add("GAC");
+    Asp.add("GAT");
+
+    Tyr.add("TAC");
+    Tyr.add("TAT");
+
+    Thr.add("ACA");
+    Thr.add("ACG");
+    Thr.add("ACC");
+    Thr.add("ACT");
+
+    Pro.add("CCA");
+    Pro.add("CCG");
+    Pro.add("CCC");
+    Pro.add("CCT");
+
+    Ala.add("GCA");
+    Ala.add("GCG");
+    Ala.add("GCC");
+    Ala.add("GCT");
+
+    Ser.add("TCA");
+    Ser.add("TCG");
+    Ser.add("TCC");
+    Ser.add("TCT");
+    Ser.add("AGC");
+    Ser.add("AGT");
+
+    Arg.add("AGA");
+    Arg.add("AGG");
+    Arg.add("CGA");
+    Arg.add("CGG");
+    Arg.add("CGC");
+    Arg.add("CGT");
+
+    Gly.add("GGA");
+    Gly.add("GGG");
+    Gly.add("GGC");
+    Gly.add("GGT");
 
     STOP.add("TGA");
     STOP.add("TAA");
     STOP.add("TAG");
 
-    Trp.addElement("TGG");
+    Trp.add("TGG");
 
-    Cys.addElement("TGC");
-    Cys.addElement("TGT");
+    Cys.add("TGC");
+    Cys.add("TGT");
 
-    Ile.addElement("ATA");
-    Ile.addElement("ATC");
-    Ile.addElement("ATT");
+    Ile.add("ATA");
+    Ile.add("ATC");
+    Ile.add("ATT");
 
-    Met.addElement("ATG");
+    Met.add("ATG");
 
-    Leu.addElement("CTA");
-    Leu.addElement("CTG");
-    Leu.addElement("CTC");
-    Leu.addElement("CTT");
-    Leu.addElement("TTA");
-    Leu.addElement("TTG");
+    Leu.add("CTA");
+    Leu.add("CTG");
+    Leu.add("CTC");
+    Leu.add("CTT");
+    Leu.add("TTA");
+    Leu.add("TTG");
 
-    Val.addElement("GTA");
-    Val.addElement("GTG");
-    Val.addElement("GTC");
-    Val.addElement("GTT");
+    Val.add("GTA");
+    Val.add("GTG");
+    Val.add("GTC");
+    Val.add("GTT");
 
-    Phe.addElement("TTC");
-    Phe.addElement("TTT");
+    Phe.add("TTC");
+    Phe.add("TTT");
   }
 
   // Stores residue codes/names and colours and other things
@@ -1594,14 +1594,9 @@ public class ResidueProperties
     {
       return "X";
     }
-    Enumeration e = codonHash.keys();
-
-    while (e.hasMoreElements())
+    for (String key : codonHash.keySet())
     {
-      String key = (String) e.nextElement();
-      Vector tmp = (Vector) codonHash.get(key);
-
-      if (tmp.contains(codon))
+      if (codonHash.get(key).contains(codon))
       {
         return key;
       }