X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=4699dc6982efb31fab7fe9dedb31a51df4f4a677;hb=9a88b5f931393037048bf4d8c1c3b871ae585b1c;hp=87efddc2d927e5126859386eeae669d5a345bef4;hpb=af5db81aeed0fb115a5c808275cf2d5c1b6cc139;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 87efddc..4699dc6 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -25,90 +25,99 @@ import java.awt.*;
 public class ResidueProperties
 {
   //Stores residue codes/names and colours and other things
-  public static final Hashtable aaHash = new Hashtable(); // stores the number value of the aa
+  public static final int [] aaIndex; // aaHash version 2.1.1 and below
+  public static final int [] nucleotideIndex;
   public static final Hashtable aa3Hash = new Hashtable();
   public static final Hashtable aa2Triplet = new Hashtable();
-  public static final Hashtable nucleotideHash = new Hashtable();
   public static final Hashtable nucleotideName = new Hashtable();
 
+
   static
   {
-    aaHash.put("A", new Integer(0));
-    aaHash.put("R", new Integer(1));
-    aaHash.put("N", new Integer(2));
-    aaHash.put("D", new Integer(3));
-    aaHash.put("C", new Integer(4));
-    aaHash.put("Q", new Integer(5));
-    aaHash.put("E", new Integer(6));
-    aaHash.put("G", new Integer(7));
-    aaHash.put("H", new Integer(8));
-    aaHash.put("I", new Integer(9));
-    aaHash.put("L", new Integer(10));
-    aaHash.put("K", new Integer(11));
-    aaHash.put("M", new Integer(12));
-    aaHash.put("F", new Integer(13));
-    aaHash.put("P", new Integer(14));
-    aaHash.put("S", new Integer(15));
-    aaHash.put("T", new Integer(16));
-    aaHash.put("W", new Integer(17));
-    aaHash.put("Y", new Integer(18));
-    aaHash.put("V", new Integer(19));
-    aaHash.put("B", new Integer(20));
-    aaHash.put("Z", new Integer(21));
-    aaHash.put("X", new Integer(22));
-    aaHash.put("U", new Integer(22));
-    aaHash.put("a", new Integer(0));
-    aaHash.put("r", new Integer(1));
-    aaHash.put("n", new Integer(2));
-    aaHash.put("d", new Integer(3));
-    aaHash.put("c", new Integer(4));
-    aaHash.put("q", new Integer(5));
-    aaHash.put("e", new Integer(6));
-    aaHash.put("g", new Integer(7));
-    aaHash.put("h", new Integer(8));
-    aaHash.put("i", new Integer(9));
-    aaHash.put("l", new Integer(10));
-    aaHash.put("k", new Integer(11));
-    aaHash.put("m", new Integer(12));
-    aaHash.put("f", new Integer(13));
-    aaHash.put("p", new Integer(14));
-    aaHash.put("s", new Integer(15));
-    aaHash.put("t", new Integer(16));
-    aaHash.put("w", new Integer(17));
-    aaHash.put("y", new Integer(18));
-    aaHash.put("v", new Integer(19));
-    aaHash.put("b", new Integer(20));
-    aaHash.put("z", new Integer(21));
-    aaHash.put("x", new Integer(22));
-    aaHash.put("u", new Integer(22));
-    aaHash.put("-", new Integer(23));
-    aaHash.put("*", new Integer(23));
-    aaHash.put(".", new Integer(23));
-    aaHash.put(" ", new Integer(23));
+    aaIndex = new int[132];
+    for(int i=0; i<132; i++)
+      aaIndex[i] = -1;
+
+    aaIndex['A'] = 0;
+    aaIndex['R'] = 1;
+    aaIndex['N'] = 2;
+    aaIndex['D'] = 3;
+    aaIndex['C'] = 4;
+    aaIndex['Q'] = 5;
+    aaIndex['E'] = 6;
+    aaIndex['G'] = 7;
+    aaIndex['H'] = 8;
+    aaIndex['I'] = 9;
+    aaIndex['L'] = 10;
+    aaIndex['K'] = 11;
+    aaIndex['M'] = 12;
+    aaIndex['F'] = 13;
+    aaIndex['P'] = 14;
+    aaIndex['S'] = 15;
+    aaIndex['T'] = 16;
+    aaIndex['W'] = 17;
+    aaIndex['Y'] = 18;
+    aaIndex['V'] = 19;
+    aaIndex['B'] = 20;
+    aaIndex['Z'] = 21;
+    aaIndex['X'] = 22;
+    aaIndex['U'] = 22;
+    aaIndex['a'] = 0;
+    aaIndex['r'] = 1;
+    aaIndex['n'] = 2;
+    aaIndex['d'] = 3;
+    aaIndex['c'] = 4;
+    aaIndex['q'] = 5;
+    aaIndex['e'] = 6;
+    aaIndex['g'] = 7;
+    aaIndex['h'] = 8;
+    aaIndex['i'] = 9;
+    aaIndex['l'] = 10;
+    aaIndex['k'] = 11;
+    aaIndex['m'] = 12;
+    aaIndex['f'] = 13;
+    aaIndex['p'] = 14;
+    aaIndex['s'] = 15;
+    aaIndex['t'] = 16;
+    aaIndex['w'] = 17;
+    aaIndex['y'] = 18;
+    aaIndex['v'] = 19;
+    aaIndex['b'] = 20;
+    aaIndex['z'] = 21;
+    aaIndex['x'] = 22;
+    aaIndex['u'] = 22;
+    aaIndex['-'] = 23;
+    aaIndex['*'] = 23;
+    aaIndex['.'] = 23;
+    aaIndex[' '] = 23;
   }
 
   static
   {
-    nucleotideHash.put("A", new Integer(0));
-    nucleotideHash.put("a", new Integer(0));
-    nucleotideHash.put("C", new Integer(1));
-    nucleotideHash.put("c", new Integer(1));
-    nucleotideHash.put("G", new Integer(2));
-    nucleotideHash.put("g", new Integer(2));
-    nucleotideHash.put("T", new Integer(3));
-    nucleotideHash.put("t", new Integer(3));
-    nucleotideHash.put("U", new Integer(4));
-    nucleotideHash.put("u", new Integer(4));
-    nucleotideHash.put("I", new Integer(5));
-    nucleotideHash.put("i", new Integer(5));
-    nucleotideHash.put("X", new Integer(6));
-    nucleotideHash.put("x", new Integer(6));
-    nucleotideHash.put("R", new Integer(7));
-    nucleotideHash.put("r", new Integer(7));
-    nucleotideHash.put("Y", new Integer(8));
-    nucleotideHash.put("y", new Integer(8));
-    nucleotideHash.put("N", new Integer(9));
-    nucleotideHash.put("n", new Integer(9));
+    nucleotideIndex = new int[132];
+    for (int i = 0; i < 132; i++)
+      nucleotideIndex[i] = -1;
+
+    nucleotideIndex['A'] = 0;
+    nucleotideIndex['a'] = 0;
+    nucleotideIndex['C'] = 1;
+    nucleotideIndex['c'] = 1;
+    nucleotideIndex['G'] = 2;
+    nucleotideIndex['g'] = 2;
+    nucleotideIndex['T'] = 3;
+    nucleotideIndex['t'] = 3;
+    nucleotideIndex['U'] = 4;
+    nucleotideIndex['u'] = 4;
+    nucleotideIndex['I'] = 5;
+    nucleotideIndex['i'] = 5;
+    nucleotideIndex['X'] = 6;
+    nucleotideIndex['x'] = 6;
+    nucleotideIndex['R'] = 7;
+    nucleotideIndex['r'] = 7;
+    nucleotideIndex['Y'] = 8;
+    nucleotideIndex['y'] = 8;
+    nucleotideIndex['N'] = 9;
+    nucleotideIndex['n'] = 9;
 
 
     nucleotideName.put("A", "Adenine");
@@ -1134,11 +1143,6 @@ public class ResidueProperties
     return hyd;
   }
 
-  public static Hashtable getAAHash()
-  {
-    return aaHash;
-  }
-
   public static Hashtable getAA3Hash()
   {
     return aa3Hash;
@@ -1156,9 +1160,10 @@ public class ResidueProperties
 
   public static int getPAM250(String A1, String A2)
   {
-    Integer pog1 = (Integer) aaHash.get(A1);
-    Integer pog2 = (Integer) aaHash.get(A2);
-    int pog = ResidueProperties.PAM250[pog1.intValue()][pog2.intValue()];
+    int a = aaIndex[A1.charAt(0)];
+    int b = aaIndex[A2.charAt(0)];
+
+    int pog = ResidueProperties.PAM250[a][b];
 
     return pog;
   }
@@ -1169,9 +1174,10 @@ public class ResidueProperties
 
     try
     {
-      Integer pog1 = (Integer) aaHash.get(A1);
-      Integer pog2 = (Integer) aaHash.get(A2);
-      pog = ResidueProperties.BLOSUM62[pog1.intValue()][pog2.intValue()];
+      int a = aaIndex[A1.charAt(0)];
+      int b = aaIndex[A2.charAt(0)];
+
+      pog = ResidueProperties.BLOSUM62[a][b];
     }
     catch (Exception e)
     {