It would be fine to add them there too. You'd still need to modify the SCF parser though in order for it to be able to know about them.
cheers, Richard 2008/10/31 Ben Berman <[EMAIL PROTECTED]>: > > Is there a reason why IUPAC ambiguity codes have never been added to > DNATools? Would it hurt the performance of symbol lookups? > > > On Oct 31, 2008, at 3:05 AM, [EMAIL PROTECTED] wrote: > >> Hello, >> >> >> I am using the SCF class in the context of HIV-1 population sequencing. In >> this context we do have sometimes ambiguous base calls. To support them I >> extended the SCF class to allow for IUPAC ambiguities up to 2 nucleotides. >> >> Therefore I simply added the following code to the "decode" function: >> >> ######################### >> public Symbol decode(byte call) throws IllegalSymbolException { >> >> //get the DNA Alphabet >> Alphabet dna = DNATools.getDNA(); >> >> char c = (char) call; >> switch (c) { >> case 'a': >> case 'A': >> return DNATools.a(); >> case 'c': >> case 'C': >> return DNATools.c(); >> case 'g': >> case 'G': >> return DNATools.g(); >> case 't': >> case 'T': >> return DNATools.t(); >> case 'n': >> case 'N': >> return DNATools.n(); >> case '-': >> return DNATools.getDNA().getGapSymbol(); >> case 'w': >> case 'W': >> //make the 'W' symbol >> Set symbolsThatMakeW = new HashSet(); >> symbolsThatMakeW.add(DNATools.a()); >> symbolsThatMakeW.add(DNATools.t()); >> Symbol w = dna.getAmbiguity(symbolsThatMakeW); >> return w; >> case 's': >> case 'S': >> //make the 'S' symbol >> Set symbolsThatMakeS = new HashSet(); >> symbolsThatMakeS.add(DNATools.c()); >> symbolsThatMakeS.add(DNATools.g()); >> Symbol s = dna.getAmbiguity(symbolsThatMakeS); >> return s; >> ... (and so on) >> ######################### >> >> Is this the right way to do it? And if so, how can this code be submitted >> to >> the official biojava source code? >> >> >> Best regards, >> Daniel Struck >> _________________________________________________________ >> Mail sent using root eSolutions Webmailer - www.root.lu >> >> >> _______________________________________________ >> Biojava-l mailing list - Biojava-l@lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biojava-l >> > > ---- > Ben Berman, PhD > Research Associate, USC Epigenome Center > Harlyne J. Norris Research Tower > 1450 Biggy St. > Room #G511, MC 9601 > Los Angeles, CA 90033 > > _______________________________________________ > Biojava-l mailing list - Biojava-l@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: [EMAIL PROTECTED] http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l