From 36ddc5873f52fc3f38aa2605446a0cd77ca94070 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 22 Aug 2005 17:03:14 +0000
Subject: [PATCH] finalize all these hashtables

---
 src/jalview/schemes/ResidueProperties.java |   56 ++++++++++++++--------------
 1 file changed, 28 insertions(+), 28 deletions(-)

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 0b71381..8b1d92b 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -25,10 +25,10 @@ import java.awt.*;
 public class ResidueProperties
 {
   //Stores residue codes/names and colours and other things
-  public static Hashtable aaHash = new Hashtable(); // stores the number value of the aa
-  public static Hashtable aa3Hash = new Hashtable();
-  public static Hashtable aa2Triplet = new Hashtable();
-  public static Hashtable nucleotideHash = new Hashtable();
+  public static final Hashtable aaHash = new Hashtable(); // stores the number value of the aa
+  public static final Hashtable aa3Hash = new Hashtable();
+  public static final Hashtable aa2Triplet = new Hashtable();
+  public static final Hashtable nucleotideHash = new Hashtable();
 
   static
   {
@@ -94,7 +94,7 @@ public class ResidueProperties
   }
 
   // These numbers should correspond to the indices in the Color hashes
-  public static Hashtable aaSpecialsHash = new Hashtable();
+  public static final Hashtable aaSpecialsHash = new Hashtable();
 
   static
   {
@@ -179,13 +179,13 @@ public class ResidueProperties
     aa2Triplet.put("v", "VAL");
   }
 
-  public static String[] aa =
+  public static final String[] aa =
       {
       "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
       "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " "
   };
-  public static Color midBlue = new Color(100, 100, 255);
-  public static Vector scaleColours = new Vector();
+  public static final Color midBlue = new Color(100, 100, 255);
+  public static final Vector scaleColours = new Vector();
 
   static
   {
@@ -201,7 +201,7 @@ public class ResidueProperties
     scaleColours.addElement(Color.white);
   }
 
-  public static Color[] taylor =
+  public static final Color[] taylor =
       {
       new Color(204, 255, 0), // A  Greenish-yellowy-yellow
       new Color(0, 0, 255), // R  Blueish-bluey-blue
@@ -230,7 +230,7 @@ public class ResidueProperties
       Color.white, // *
       Color.white // .
   };
-  public static Color[] nucleotide =
+  public static final Color[] nucleotide =
       {
       new Color(100, 247, 63), // A
       new Color(255, 179, 64), // C
@@ -238,7 +238,7 @@ public class ResidueProperties
       new Color(60, 136, 238), // T
       new Color(60, 136, 238) // U
   };
-  public static Color[] color =
+  public static final Color[] color =
       {
       Color.pink, // A
       midBlue, // R
@@ -270,7 +270,7 @@ public class ResidueProperties
   };
 
   // Dunno where I got these numbers from
-  public static double[] hyd2 =
+  public static final double[] hyd2 =
       {
       0.62, //A
       0.29, //R
@@ -296,39 +296,39 @@ public class ResidueProperties
       0.0, //Z
       0.0 //X
   };
-  public static double[] helix =
+  public static final double[] helix =
       {
       1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16,
       1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0
   };
-  public static double helixmin = 0.57;
-  public static double helixmax = 1.51;
-  public static double[] strand =
+  public static final double helixmin = 0.57;
+  public static final double helixmax = 1.51;
+  public static final double[] strand =
       {
       0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74,
       1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0
   };
-  public static double strandmin = 0.37;
-  public static double strandmax = 1.7;
-  public static double[] turn =
+  public static final double strandmin = 0.37;
+  public static final double strandmax = 1.7;
+  public static final double[] turn =
       {
       0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01,
       0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0
   };
-  public static double turnmin = 0.47;
-  public static double turnmax = 1.56;
-  public static double[] buried =
+  public static final double turnmin = 0.47;
+  public static final double turnmax = 1.56;
+  public static final double[] buried =
       {
       1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2,
       0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00
   };
-  public static double buriedmin = 0.05;
-  public static double buriedmax = 4.6;
+  public static final double buriedmin = 0.05;
+  public static final double buriedmax = 4.6;
 
   // This is hydropathy index
   // Kyte, J., and Doolittle, R.F., J. Mol. Biol.
   // 1157, 105-132, 1982
-  public static double[] hyd =
+  public static final double[] hyd =
       {
       1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9,
       2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0
@@ -536,7 +536,7 @@ public class ResidueProperties
       -8, -8, -8, -8, -8, -8, 1
   },
   };
-  public static Hashtable ssHash = new Hashtable(); // stores the number value of the aa
+  public static final Hashtable ssHash = new Hashtable(); // stores the number value of the aa
 
   static
   {
@@ -564,13 +564,13 @@ public class ResidueProperties
       {
       1, 1, 1, 1, 1}, // -
   };
-  public static Color[] pidColours =
+  public static final Color[] pidColours =
       {
       midBlue, new Color(153, 153, 255),
       //    Color.lightGray,
       new Color(204, 204, 255),
   };
-  public static float[] pidThresholds =
+  public static final float[] pidThresholds =
       {
       80, 60, 40, };
   public static Hashtable codonHash = new Hashtable();
-- 
1.7.10.2