X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=98868d23a38fdd13c4a82c407ed5efeff4345414;hb=ccc0d91abe38690088a6050faba8ef66cde1f271;hp=17f6a410dbfe88e8e5c38ad973173e43447f5cb4;hpb=558597672640984d936ea22409a674293192a09c;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 17f6a41..98868d2 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) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -24,20 +24,21 @@ import java.awt.*;
 
 public class ResidueProperties
 {
-  public static Hashtable scoreMatrices=new Hashtable();
+  public static Hashtable scoreMatrices = new Hashtable();
   //Stores residue codes/names and colours and other things
-  public static final int [] aaIndex; // aaHash version 2.1.1 and below
-  public static final int [] nucleotideIndex;
+  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
   {
     aaIndex = new int[255];
-    for(int i=0; i<255; i++)
+    for (int i = 0; i < 255; i++)
+    {
       aaIndex[i] = 23;
+    }
 
     aaIndex['A'] = 0;
     aaIndex['R'] = 1;
@@ -86,14 +87,16 @@ public class ResidueProperties
     aaIndex['b'] = 20;
     aaIndex['z'] = 21;
     aaIndex['x'] = 22;
-    aaIndex['u'] = 22;
+    aaIndex['u'] = 22; // TODO: selenocystine triplet and codons needed. also extend subt. matrices
   }
 
   static
   {
     nucleotideIndex = new int[255];
     for (int i = 0; i < 255; i++)
+    {
       nucleotideIndex[i] = -1;
+    }
 
     nucleotideIndex['A'] = 0;
     nucleotideIndex['a'] = 0;
@@ -116,7 +119,6 @@ public class ResidueProperties
     nucleotideIndex['N'] = 9;
     nucleotideIndex['n'] = 9;
 
-
     nucleotideName.put("A", "Adenine");
     nucleotideName.put("a", "Adenine");
     nucleotideName.put("G", "Guanine");
@@ -139,7 +141,6 @@ public class ResidueProperties
     nucleotideName.put("n", "Unknown");
   }
 
-
   static
   {
     aa3Hash.put("ALA", new Integer(0));
@@ -165,7 +166,7 @@ public class ResidueProperties
     // 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("XAA", new Integer(22)); // X unknown
     aa3Hash.put("-", new Integer(23));
     aa3Hash.put("*", new Integer(23));
     aa3Hash.put(".", new Integer(23));
@@ -276,7 +277,8 @@ public class ResidueProperties
       new Color(60, 136, 238), // T
       new Color(60, 136, 238) // U
   };
-  public static final Color[] color =
+  // Zappo
+  public static final Color[] zappo =
       {
       Color.pink, // A
       midBlue, // R
@@ -286,7 +288,7 @@ public class ResidueProperties
       Color.green, // Q
       Color.red, // E
       Color.magenta, // G
-      Color.red, // H
+      midBlue,// Color.red, // H
       Color.pink, // I
       Color.pink, // L
       midBlue, // K
@@ -605,11 +607,13 @@ public class ResidueProperties
   /**
    * register matrices in list
    */
-  static {
-    scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62",BLOSUM62, 0));
-    scoreMatrices.put("PAM250", new ScoreMatrix("PAM250",PAM250, 0));
+  static
+  {
+    scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62", BLOSUM62, 0));
+    scoreMatrices.put("PAM250", new ScoreMatrix("PAM250", PAM250, 0));
     scoreMatrices.put("DNA", new ScoreMatrix("DNA", DNA, 1));
   }
+
   public static final Color[] pidColours =
       {
       midBlue, new Color(153, 153, 255),
@@ -839,7 +843,6 @@ public class ResidueProperties
     Phe.addElement("TTT");
   }
 
-
   //Stores residue codes/names and colours and other things
   public static Hashtable propHash = new Hashtable();
   public static Hashtable hydrophobic = new Hashtable();
@@ -1165,12 +1168,7 @@ public class ResidueProperties
 
   public static int getPAM250(String A1, String A2)
   {
-    int a = aaIndex[A1.charAt(0)];
-    int b = aaIndex[A2.charAt(0)];
-
-    int pog = ResidueProperties.PAM250[a][b];
-
-    return pog;
+    return getPAM250(A1.charAt(0), A2.charAt(0));
   }
 
   public static int getBLOSUM62(char c1, char c2)
@@ -1220,10 +1218,13 @@ public class ResidueProperties
     return null;
   }
 
-  public static int[][] getDefaultPeptideMatrix() {
+  public static int[][] getDefaultPeptideMatrix()
+  {
     return ResidueProperties.getBLOSUM62();
   }
-  public static int[][] getDefaultDnaMatrix() {
+
+  public static int[][] getDefaultDnaMatrix()
+  {
     return ResidueProperties.getDNA();
   }
 
@@ -1232,10 +1233,110 @@ public class ResidueProperties
    * @param pwtype
    * @return matrix in scoreMatrices with key pwtype or null
    */
-  public static ScoreMatrix getScoreMatrix(String pwtype) {
-    Object val=scoreMatrices.get(pwtype);
-    if (val!=null)
+  public static ScoreMatrix getScoreMatrix(String pwtype)
+  {
+    Object val = scoreMatrices.get(pwtype);
+    if (val != null)
+    {
       return (ScoreMatrix) val;
+    }
     return null;
   }
+
+  public static int getPAM250(char c, char d)
+  {
+    int a = aaIndex[c];
+    int b = aaIndex[d];
+
+    int pog = ResidueProperties.PAM250[a][b];
+
+    return pog;
+  }
+
+  public static Hashtable toDssp3State;
+  static {
+    toDssp3State = new Hashtable();
+    toDssp3State.put("H", "H");
+    toDssp3State.put("E", "E");
+    toDssp3State.put("C", " ");
+    toDssp3State.put(" ", " ");
+    toDssp3State.put("T", " ");
+    toDssp3State.put("B", "E");
+    toDssp3State.put("G", "H");
+    toDssp3State.put("I", "H");
+    toDssp3State.put("X", " ");
+  }
+  /**
+   * translate from other dssp secondary structure alphabets to 3-state
+   * @param ssstring
+   * @return ssstring as a three-state secondary structure assignment.
+   */
+  public static String getDssp3state(String ssstring)
+  {
+    if (ssstring==null)
+    {
+      return null;
+    }
+    StringBuffer ss = new StringBuffer();
+    for (int i=0; i<ssstring.length(); i++)
+    {
+      String ssc = ssstring.substring(i, i+1);
+      if (toDssp3State.containsKey(ssc))
+      {
+        ss.append((String) toDssp3State.get(ssc));
+      } else {
+        ss.append(" ");
+      }
+    }
+    return ss.toString();
+  }
+  // main method generates perl representation of residue property hash
+  /// cut here
+  public static void main(String[] args)
+  {
+    Hashtable aa = new Hashtable(); 
+    System.out.println("my %aa = {");
+    // invert property hashes
+    Enumeration prop = propHash.keys();
+    while (prop.hasMoreElements())
+    {
+      String pname = (String) prop.nextElement();
+      Hashtable phash = (Hashtable) propHash.get(pname);
+      Enumeration res = phash.keys();
+      while (res.hasMoreElements())
+      {
+        String rname = (String) res.nextElement();
+        Vector aprops = (Vector) aa.get(rname);
+        if (aprops==null)
+        {
+          aprops = new Vector();
+          aa.put(rname, aprops);
+        }
+        Integer hasprop = (Integer) phash.get(rname);
+        if (hasprop.intValue()==1)
+        {
+          aprops.addElement(pname);
+        }
+      }
+    }
+    Enumeration res = aa.keys();
+    while (res.hasMoreElements())
+    {
+      String rname = (String) res.nextElement();
+      
+      System.out.print("'"+rname+"' => [");
+      Enumeration props = ((Vector) aa.get(rname)).elements();
+      while (props.hasMoreElements())
+      {
+        System.out.print("'"+(String)props.nextElement()+"'");
+        if (props.hasMoreElements())
+        {
+          System.out.println(", ");
+        }
+      }
+      System.out.println("]"+(res.hasMoreElements() ? "," : ""));
+    }
+    System.out.println("};");
+  }
+  // to here
 }