2.08, not 2.07

[jalview.git] / src / jalview / schemes / ResidueProperties.java

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 8b1d92b..65cc0f1 100755 (executable)
--- 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();\r
   public static final Hashtable aa2Triplet = new Hashtable();\r
   public static final Hashtable nucleotideHash = new Hashtable();\r
+  public static final Hashtable nucleotideName = new Hashtable();\r
 \r
   static\r
   {\r
@@ -55,6 +56,7 @@ public class ResidueProperties
     aaHash.put("B", new Integer(20));\r
     aaHash.put("Z", new Integer(21));\r
     aaHash.put("X", new Integer(22));\r
+    aaHash.put("U", new Integer(22));\r
     aaHash.put("a", new Integer(0));\r
     aaHash.put("r", new Integer(1));\r
     aaHash.put("n", new Integer(2));\r
@@ -78,6 +80,7 @@ public class ResidueProperties
     aaHash.put("b", new Integer(20));\r
     aaHash.put("z", new Integer(21));\r
     aaHash.put("x", new Integer(22));\r
+    aaHash.put("u", new Integer(22));\r
     aaHash.put("-", new Integer(23));\r
     aaHash.put("*", new Integer(23));\r
     aaHash.put(".", new Integer(23));\r
@@ -87,22 +90,49 @@ public class ResidueProperties
   static\r
   {\r
     nucleotideHash.put("A", new Integer(0));\r
+    nucleotideHash.put("a", new Integer(0));\r
     nucleotideHash.put("C", new Integer(1));\r
+    nucleotideHash.put("c", new Integer(1));\r
     nucleotideHash.put("G", new Integer(2));\r
+    nucleotideHash.put("g", new Integer(2));\r
     nucleotideHash.put("T", new Integer(3));\r
+    nucleotideHash.put("t", new Integer(3));\r
     nucleotideHash.put("U", new Integer(4));\r
+    nucleotideHash.put("u", new Integer(4));\r
+    nucleotideHash.put("I", new Integer(5));\r
+    nucleotideHash.put("i", new Integer(5));\r
+    nucleotideHash.put("X", new Integer(6));\r
+    nucleotideHash.put("x", new Integer(6));\r
+    nucleotideHash.put("R", new Integer(7));\r
+    nucleotideHash.put("r", new Integer(7));\r
+    nucleotideHash.put("Y", new Integer(8));\r
+    nucleotideHash.put("y", new Integer(8));\r
+    nucleotideHash.put("N", new Integer(9));\r
+    nucleotideHash.put("n", new Integer(9));\r
+\r
+\r
+    nucleotideName.put("A", "Adenine");\r
+    nucleotideName.put("a", "Adenine");\r
+    nucleotideName.put("G", "Guanine");\r
+    nucleotideName.put("g", "Guanine");\r
+    nucleotideName.put("C", "Cytosine");\r
+    nucleotideName.put("c", "Cytosine");\r
+    nucleotideName.put("T", "Thymine");\r
+    nucleotideName.put("t", "Thymine");\r
+    nucleotideName.put("U", "Uracil");\r
+    nucleotideName.put("u", "Uracil");\r
+    nucleotideName.put("I", "Inosine");\r
+    nucleotideName.put("i", "Inosine");\r
+    nucleotideName.put("X", "Xanthine");\r
+    nucleotideName.put("x", "Xanthine");\r
+    nucleotideName.put("R", "Unknown Purine");\r
+    nucleotideName.put("r", "Unknown Purine");\r
+    nucleotideName.put("Y", "Unknown Pyrimidine");\r
+    nucleotideName.put("y", "Unknown Pyrimidine");\r
+    nucleotideName.put("N", "Unknown");\r
+    nucleotideName.put("n", "Unknown");\r
   }\r
 \r
-  // These numbers should correspond to the indices in the Color hashes\r
-  public static final Hashtable aaSpecialsHash = new Hashtable();\r
-\r
-  static\r
-  {\r
-    aaSpecialsHash.put("-", new Integer(23));\r
-    aaSpecialsHash.put("*", new Integer(24));\r
-    aaSpecialsHash.put(".", new Integer(25));\r
-    aaSpecialsHash.put(" ", new Integer(26));\r
-  }\r
 \r
   static\r
   {\r
@@ -126,9 +156,10 @@ public class ResidueProperties
     aa3Hash.put("TRP", new Integer(17));\r
     aa3Hash.put("TYR", new Integer(18));\r
     aa3Hash.put("VAL", new Integer(19));\r
-    aa3Hash.put("B", new Integer(20));\r
-    aa3Hash.put("Z", new Integer(21));\r
-    aa3Hash.put("X", new Integer(22));\r
+    // IUB Nomenclature for ambiguous peptides\r
+    aa3Hash.put("ASX", new Integer(20)); // "B";\r
+    aa3Hash.put("GLX", new Integer(21)); // X\r
+    aa3Hash.put("XAA", new Integer(22));// X unknown\r
     aa3Hash.put("-", new Integer(23));\r
     aa3Hash.put("*", new Integer(23));\r
     aa3Hash.put(".", new Integer(23));\r
@@ -793,27 +824,6 @@ public class ResidueProperties
     Phe.addElement("TTT");\r
   }\r
 \r
-  public static Color[][] groupColors =\r
-      {\r
-      {\r
-      Color.red, Color.red.brighter(), Color.red.brighter().brighter()},\r
-      {\r
-      Color.orange, Color.orange.brighter(),\r
-      Color.orange.brighter().brighter()\r
-  },\r
-      {\r
-      Color.green, Color.green.brighter(), Color.green.brighter().brighter()},\r
-      {\r
-      Color.blue, Color.blue.brighter(), Color.blue.brighter().brighter()},\r
-      {\r
-      Color.magenta, Color.magenta.brighter(),\r
-      Color.magenta.brighter().brighter()\r
-  },\r
-      {\r
-      Color.cyan, Color.cyan.brighter(), Color.cyan.brighter().brighter()},\r
-      {\r
-      Color.pink, Color.pink.brighter(), Color.pink.brighter().brighter()},\r
-  };\r
 \r
   //Stores residue codes/names and colours and other things\r
   public static Hashtable propHash = new Hashtable();\r
@@ -1104,20 +1114,6 @@ public class ResidueProperties
     propHash.put("polar", polar);\r
   }\r
 \r
-  public static Hashtable chainColours = new Hashtable();\r
-\r
-  static\r
-  {\r
-    chainColours.put("A", Color.red);\r
-    chainColours.put("B", Color.orange);\r
-    chainColours.put("C", Color.yellow);\r
-    chainColours.put("D", Color.green);\r
-    chainColours.put("E", Color.cyan);\r
-    chainColours.put("F", Color.blue);\r
-    chainColours.put("G", Color.magenta);\r
-    chainColours.put("H", Color.pink);\r
-  }\r
-\r
   private ResidueProperties()\r
   {\r
   }\r
@@ -1203,7 +1199,7 @@ public class ResidueProperties
       String key = (String) e.nextElement();\r
       Vector tmp = (Vector) codonHash.get(key);\r
 \r
-      if (tmp.contains(codon))\r
+      if (tmp.contains(codon.toUpperCase()))\r
       {\r
         return key;\r
       }\r
@@ -1211,9 +1207,4 @@ public class ResidueProperties
 \r
     return null;\r
   }\r
-\r
-  public static Hashtable getChainColours()\r
-  {\r
-    return chainColours;\r
-  }\r
 }\r