[Biojava-l] SCF: support for ambiguities

[community at struck.lu]

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" <holland at eaglegenomics.com> 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 community at struck.lu <community at struck.lu>:
> > 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 at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
> 
> 


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