finalize all these hashtables

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