X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=4699dc6982efb31fab7fe9dedb31a51df4f4a677;hb=9a88b5f931393037048bf4d8c1c3b871ae585b1c;hp=0b71381a2a027b7819a8e5ec844208ed02a25c4f;hpb=96786b7b949dc261a9556e13a17870166915d0e9;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 0b71381..4699dc6 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -25,85 +25,124 @@ 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 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 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("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("-", new Integer(23));
-    aaHash.put("*", new Integer(23));
-    aaHash.put(".", new Integer(23));
-    aaHash.put(" ", new Integer(23));
-  }
 
   static
   {
-    nucleotideHash.put("A", new Integer(0));
-    nucleotideHash.put("C", new Integer(1));
-    nucleotideHash.put("G", new Integer(2));
-    nucleotideHash.put("T", new Integer(3));
-    nucleotideHash.put("U", new Integer(4));
+    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;
   }
 
-  // These numbers should correspond to the indices in the Color hashes
-  public static Hashtable aaSpecialsHash = new Hashtable();
-
   static
   {
-    aaSpecialsHash.put("-", new Integer(23));
-    aaSpecialsHash.put("*", new Integer(24));
-    aaSpecialsHash.put(".", new Integer(25));
-    aaSpecialsHash.put(" ", new Integer(26));
+    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");
+    nucleotideName.put("a", "Adenine");
+    nucleotideName.put("G", "Guanine");
+    nucleotideName.put("g", "Guanine");
+    nucleotideName.put("C", "Cytosine");
+    nucleotideName.put("c", "Cytosine");
+    nucleotideName.put("T", "Thymine");
+    nucleotideName.put("t", "Thymine");
+    nucleotideName.put("U", "Uracil");
+    nucleotideName.put("u", "Uracil");
+    nucleotideName.put("I", "Inosine");
+    nucleotideName.put("i", "Inosine");
+    nucleotideName.put("X", "Xanthine");
+    nucleotideName.put("x", "Xanthine");
+    nucleotideName.put("R", "Unknown Purine");
+    nucleotideName.put("r", "Unknown Purine");
+    nucleotideName.put("Y", "Unknown Pyrimidine");
+    nucleotideName.put("y", "Unknown Pyrimidine");
+    nucleotideName.put("N", "Unknown");
+    nucleotideName.put("n", "Unknown");
   }
 
+
   static
   {
     aa3Hash.put("ALA", new Integer(0));
@@ -126,13 +165,15 @@ public class ResidueProperties
     aa3Hash.put("TRP", new Integer(17));
     aa3Hash.put("TYR", new Integer(18));
     aa3Hash.put("VAL", new Integer(19));
-    aa3Hash.put("B", new Integer(20));
-    aa3Hash.put("Z", new Integer(21));
-    aa3Hash.put("X", new Integer(22));
+    // IUB Nomenclature for ambiguous peptides
+    aa3Hash.put("ASX", new Integer(20)); // "B";
+    aa3Hash.put("GLX", new Integer(21)); // X
+    aa3Hash.put("XAA", new Integer(22));// X unknown
     aa3Hash.put("-", new Integer(23));
     aa3Hash.put("*", new Integer(23));
     aa3Hash.put(".", new Integer(23));
     aa3Hash.put(" ", new Integer(23));
+    aa3Hash.put("Gap", new Integer(23));
   }
 
   static
@@ -179,13 +220,13 @@ 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 +242,7 @@ 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 +271,7 @@ 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 +279,7 @@ 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 +311,7 @@ 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 +337,39 @@ 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 +577,7 @@ 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 +605,13 @@ 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();
@@ -793,27 +834,6 @@ public class ResidueProperties
     Phe.addElement("TTT");
   }
 
-  public static Color[][] groupColors =
-      {
-      {
-      Color.red, Color.red.brighter(), Color.red.brighter().brighter()},
-      {
-      Color.orange, Color.orange.brighter(),
-      Color.orange.brighter().brighter()
-  },
-      {
-      Color.green, Color.green.brighter(), Color.green.brighter().brighter()},
-      {
-      Color.blue, Color.blue.brighter(), Color.blue.brighter().brighter()},
-      {
-      Color.magenta, Color.magenta.brighter(),
-      Color.magenta.brighter().brighter()
-  },
-      {
-      Color.cyan, Color.cyan.brighter(), Color.cyan.brighter().brighter()},
-      {
-      Color.pink, Color.pink.brighter(), Color.pink.brighter().brighter()},
-  };
 
   //Stores residue codes/names and colours and other things
   public static Hashtable propHash = new Hashtable();
@@ -1104,20 +1124,6 @@ public class ResidueProperties
     propHash.put("polar", polar);
   }
 
-  public static Hashtable chainColours = new Hashtable();
-
-  static
-  {
-    chainColours.put("A", Color.red);
-    chainColours.put("B", Color.orange);
-    chainColours.put("C", Color.yellow);
-    chainColours.put("D", Color.green);
-    chainColours.put("E", Color.cyan);
-    chainColours.put("F", Color.blue);
-    chainColours.put("G", Color.magenta);
-    chainColours.put("H", Color.pink);
-  }
-
   private ResidueProperties()
   {
   }
@@ -1137,11 +1143,6 @@ public class ResidueProperties
     return hyd;
   }
 
-  public static Hashtable getAAHash()
-  {
-    return aaHash;
-  }
-
   public static Hashtable getAA3Hash()
   {
     return aa3Hash;
@@ -1159,9 +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;
   }
@@ -1172,9 +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)
     {
@@ -1203,7 +1206,7 @@ public class ResidueProperties
       String key = (String) e.nextElement();
       Vector tmp = (Vector) codonHash.get(key);
 
-      if (tmp.contains(codon))
+      if (tmp.contains(codon.toUpperCase()))
       {
         return key;
       }
@@ -1211,9 +1214,4 @@ public class ResidueProperties
 
     return null;
   }
-
-  public static Hashtable getChainColours()
-  {
-    return chainColours;
-  }
 }