[Biojava-l] SCF: support for ambiguities

[community at struck.lu]

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" <holland at eaglegenomics.com> wrote:

> A patch would be much appreciated!
> 
> cheers,
> Richard
> 
> 2008/10/31 community at struck.lu <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
> >> >
> >>
> >>
> >
> >
> > _________________________________________________________
> > Mail sent using root eSolutions Webmailer - www.root.lu
> >
> >
> >
> 
> 


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