JAL-4019 Nucleotide Ambiguity Colour Scheme added. Test for nucleotide sequence adapt...

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 7ad35c3..73b48a9 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -20,10 +20,6 @@
  */
 package jalview.schemes;
 
-import java.util.Locale;
-
-import jalview.analysis.GeneticCodes;
-
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -31,9 +27,12 @@ import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Vector;
 
+import jalview.analysis.GeneticCodes;
+
 public class ResidueProperties
 {
   // Stores residue codes/names and colours and other things
@@ -119,74 +118,50 @@ public class ResidueProperties
   /**
    * maximum (gap) index for matrices involving nucleotide alphabet
    */
-  public final static int maxNucleotideIndex = 10;
+  // public final static int maxNucleotideIndex = 10;
+  public final static int maxNucleotideIndex;
 
   static
   {
+
+    String[][] namesArray = { { "a", "Adenine" }, { "g", "Guanine" },
+        { "c", "Cytosine" },
+        { "t", "Thymine" },
+        { "u", "Uracil" },
+        { "i", "Inosine" },
+        { "x", "Xanthine" },
+        { "r", "Unknown Purine" },
+        { "y", "Unknown Pyrimidine" },
+        { "n", "Unknown" },
+        { "w", "Weak nucleotide (A or T)" },
+        { "s", "Strong nucleotide (G or C)" },
+        { "m", "Amino (A or C)" },
+        { "k", "Keto (G or T)" },
+        { "b", "Not A (G or C or T)" },
+        { "h", "Not G (A or C or T)" },
+        { "d", "Not C (A or G or T)" },
+        { "v", "Not T (A or G or C" } };
+
+    // "gap" index
+    maxNucleotideIndex = namesArray.length + 1;
+
     nucleotideIndex = new int[255];
     for (int i = 0; i < 255; i++)
     {
-      nucleotideIndex[i] = 10; // non-nucleotide symbols are all non-gap gaps.
+      nucleotideIndex[i] = maxNucleotideIndex; // non-nucleotide symbols are all
+                                               // non-gap gaps.
     }
 
-    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");
-    nucleotideName.put("W", "Weak nucleotide (A or T)");
-    nucleotideName.put("w", "Weak nucleotide (A or T)");
-    nucleotideName.put("S", "Strong nucleotide (G or C)");
-    nucleotideName.put("s", "Strong nucleotide (G or C)");
-    nucleotideName.put("M", "Amino (A or C)");
-    nucleotideName.put("m", "Amino (A or C)");
-    nucleotideName.put("K", "Keto (G or T)");
-    nucleotideName.put("k", "Keto (G or T)");
-    nucleotideName.put("B", "Not A (G or C or T)");
-    nucleotideName.put("b", "Not A (G or C or T)");
-    nucleotideName.put("H", "Not G (A or C or T)");
-    nucleotideName.put("h", "Not G (A or C or T)");
-    nucleotideName.put("D", "Not C (A or G or T)");
-    nucleotideName.put("d", "Not C (A or G or T)");
-    nucleotideName.put("V", "Not T (A or G or C");
-    nucleotideName.put("v", "Not T (A or G or C");
-
+    for (int i = 0; i < namesArray.length; i++)
+    {
+      char c = namesArray[i][0].charAt(0);
+      nucleotideIndex[c] = i;
+      // Character.toUpperCase is Locale insensitive
+      nucleotideIndex[Character.toUpperCase(c)] = i;
+      nucleotideName.put(namesArray[i][0], namesArray[i][1]);
+      nucleotideName.put(namesArray[i][0].toUpperCase(Locale.ROOT),
+              namesArray[i][1]);
+    }
   }
 
   static
@@ -363,6 +338,36 @@ public class ResidueProperties
       Color.white, // R
       Color.white, // Y
       Color.white, // N
+      Color.white, // w
+      Color.white, // s
+      Color.white, // m
+      Color.white, // k
+      Color.white, // b
+      Color.white, // h
+      Color.white, // d
+      Color.white, // v
+      Color.white, // Gap
+  };
+
+  public static final Color[] nucleotideAmbiguity = {
+      Color.decode("#f0fff0"), // a
+      Color.decode("#f0fff0"), // g
+      Color.decode("#f0fff0"), // c
+      Color.decode("#f0fff0"), // t
+      Color.decode("#f0fff0"), // u
+      Color.decode("#ffffff"), // i
+      Color.decode("#ffffff"), // x
+      Color.decode("#CD5C5C"), // r
+      Color.decode("#008000"), // y
+      Color.decode("#2f4f4f"), // n
+      Color.decode("#4682B4"), // w
+      Color.decode("#FF8C00"), // s
+      Color.decode("#9ACD32"), // m
+      Color.decode("#9932CC"), // k
+      Color.decode("#8b4513"), // b
+      Color.decode("#808080"), // h
+      Color.decode("#483D8B"), // d
+      Color.decode("#b8860b"), // v
       Color.white, // Gap
   };