Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into...

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 2ce3e6d..f8b7856 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -140,7 +140,7 @@ public class ResidueProperties
         { "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" },
+        { "v", "Not T (A or G or C)" },
         { "n", "Unknown" } };
     // "gap" index
     maxNucleotideIndex = namesArray.length;
@@ -350,17 +350,17 @@ public class ResidueProperties
       Color.white, // Gap
   };
 
+  // this colour scheme devised by sduce
   public static final Color[] nucleotideAmbiguity = {
       Color.decode("#f0fff0"), // a
-      Color.decode("#f0fff0"), // g
       Color.decode("#f0fff0"), // c
+      Color.decode("#f0fff0"), // g
       Color.decode("#f0fff0"), // t
       Color.decode("#f0fff0"), // u
       Color.decode("#ffffff"), // i
-      Color.decode("#ffffff"), // x
+      Color.decode("#4f6f6f"), // 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
@@ -369,6 +369,7 @@ public class ResidueProperties
       Color.decode("#808080"), // h
       Color.decode("#483D8B"), // d
       Color.decode("#b8860b"), // v
+      Color.decode("#2f4f4f"), // n
       Color.white, // Gap
   };
 
@@ -2413,7 +2414,7 @@ public class ResidueProperties
   public static void main(String[] args)
   {
     Hashtable<String, Vector<String>> aaProps = new Hashtable<>();
-    System.out.println("my %aa = {");
+    jalview.bin.Console.outPrintln("my %aa = {");
     // invert property hashes
     for (String pname : propHash.keySet())
     {
@@ -2445,12 +2446,12 @@ public class ResidueProperties
         System.out.print("'" + props.nextElement() + "'");
         if (props.hasMoreElements())
         {
-          System.out.println(", ");
+          jalview.bin.Console.outPrintln(", ");
         }
       }
-      System.out.println("]" + (res.hasMoreElements() ? "," : ""));
+      jalview.bin.Console.outPrintln("]" + (res.hasMoreElements() ? "," : ""));
     }
-    System.out.println("};");
+    jalview.bin.Console.outPrintln("};");
   }
 
   // to here