public static final Map<String, String> nucleotideName = new HashMap<>();
+ public static final Map<String, String> nucleotideAmbiguityName = new HashMap<>();
+
// lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
public static final Map<String, String> modifications = new HashMap<>();
static
{
-
- String[][] namesArray = { { "a", "Adenine" }, { "g", "Guanine" },
- { "c", "Cytosine" },
+ String[][] namesArray = { { "a", "Adenine" }, { "c", "Cytosine" },
+ { "g", "Guanine" },
{ "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)" },
{ "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 + 1;
+ maxNucleotideIndex = namesArray.length;
nucleotideIndex = new int[255];
for (int i = 0; i < 255; i++)
nucleotideName.put(namesArray[i][0].toUpperCase(Locale.ROOT),
namesArray[i][1]);
}
+
}
static
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
Color.decode("#808080"), // h
Color.decode("#483D8B"), // d
Color.decode("#b8860b"), // v
+ Color.decode("#2f4f4f"), // n
Color.white, // Gap
};
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())
{
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