* Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap
*/
- public static List<String> STOP = Arrays.asList("TGA", "TAA", "TAG");
+ public static String STOP = "STOP";
+
+ public static List<String> STOP_CODONS = Arrays.asList("TGA", "TAA", "TAG");
public static String START = "ATG";
String cdn = codonHash2.get(lccodon.toUpperCase());
if ("*".equals(cdn))
{
- return "STOP";
+ return STOP;
}
return cdn;
}
amino.put('P', 0.0472f);
amino.put('V', 0.0686f);
backgroundFrequencies.put("amino", amino);
-
+ // todo: these don't match https://www.ebi.ac.uk/uniprot/TrEMBLstats - what
+ // are they?
}
// TODO get correct frequencies