Thank you, Daniel
"Richard Holland" <[EMAIL PROTECTED]> wrote: > This has now been applied to the trunk of biojava-live. > > cheers, > Richard > > 2008/11/3 Richard Holland <[EMAIL PROTECTED]>: > > Thanks for the fix. I'll review this and get back to you in a couple of > days. > > > > cheers, > > Richard > > > > 2008/11/3 [EMAIL PROTECTED] <[EMAIL PROTECTED]>: > >> I have added the missing ambiguities to DNATools.java and then used these > in > >> SCF.java. > >> The two patches are appended to this email. > >> > >> Greetings, > >> Daniel > >> > >> > >> "Richard Holland" <[EMAIL PROTECTED]> wrote: > >> > >>> A patch would be much appreciated! > >>> > >>> cheers, > >>> Richard > >>> > >>> 2008/10/31 [EMAIL PROTECTED] <[EMAIL PROTECTED]>: > >>> > True. It was a first quick and dirty hack to get the rest of my project > >>> going. > >>> > > >>> > I think adding support of the IUPAC ambiguities to DNATools would be the > >>> most > >>> > approbate solution. The SCF class can then easily be adapted. > >>> > > >>> > Are there any plans to do so? > >>> > If not, I could give it a try and submit a patch for DNATools and SCF. > >>> > > >>> > Greetings, > >>> > Daniel > >>> > > >>> > "Richard Holland" <[EMAIL PROTECTED]> wrote: > >>> > > >>> >> It is the correct method, yes. > >>> >> > >>> >> However your code constructs a new hash set every time it does the > >>> >> check for W or S etc.. It would be much more efficient to create > >>> >> class-static references to the ambiguity symbols you need, instead of > >>> >> (re)creating them every time they're encountered. A class-static gap > >>> >> symbol reference would also be good in this situation. > >>> >> > >>> >> cheers, > >>> >> Richard > >>> >> > >>> >> > >>> >> > >>> >> 2008/10/31 [EMAIL PROTECTED] <[EMAIL PROTECTED]>: > >>> >> > 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 > >>> >> > > >>> >> > >>> >> > >>> > > >>> > > >>> > _________________________________________________________ > >>> > Mail sent using root eSolutions Webmailer - www.root.lu > >>> > > >>> > > >>> > > >>> > >>> > >> > >> > >> _________________________________________________________ > >> Mail sent using root eSolutions Webmailer - www.root.lu > >> > > > > > > > > -- > > Richard Holland, BSc MBCS > > Finance Director, Eagle Genomics Ltd > > M: +44 7500 438846 | E: [EMAIL PROTECTED] > > http://www.eaglegenomics.com/ > > > > _________________________________________________________ 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