X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=65cc0f1181d99dd9d97b8e1aa4316303e9ae7c9d;hb=95789943eb181b1768a081e779a044bf595b6bf6;hp=a382662a22f87064c10cfd6632868fd2ed3e085e;hpb=8a18973f7e4521c7dd3705ebd8fabd3ca08cfcaf;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index a382662..65cc0f1 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -29,6 +29,7 @@ public class ResidueProperties
   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
   {
@@ -89,27 +90,49 @@ public class ResidueProperties
   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));
     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));
+
+
+    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");
   }
 
-  // These numbers should correspond to the indices in the Color hashes
-  public static final 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));
-  }
 
   static
   {
@@ -133,9 +156,10 @@ 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));
@@ -800,27 +824,6 @@ 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();
@@ -1111,20 +1114,6 @@ 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()
   {
   }
@@ -1210,7 +1199,7 @@ 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;
       }
@@ -1218,9 +1207,4 @@ public class ResidueProperties
 
     return null;
   }
-
-  public static Hashtable getChainColours()
-  {
-    return chainColours;
-  }
 }