Hi Keith, You can simply call sym.getMatches().size() == 0, and if true, it is a symbol with gaps. For all the cases the regex stuff will be used for any time soon, this is good enough.
Basicaly, two gaps are the same if they have the same arrangement of nested [] in their toString(). This is equivalent to them returning the same list of gap symbols in their getSymbols() methods. It's a bit complicated but it's the only way to do it without the gap rules being totaly different from all other symbols. I will add docs to package.html in Symbol explaining gaps and why they are as they are. Very quickly, the gap [] is the empty set of symbols. It means 'there is nothing to see here, move on'. [-] means 'there is nothing here and it takes up one unit of your sequence'. [-,-] would be a gap in an alignment of two sequences where both individual sequences are gapped at that point. You could also have symbols like [-,a] and [g,-] to represent gaps in one or the other sequences. For aligning things like DNA-Protein, you could end up with [-,-,-][-] (a gap in the codon and in the protein sequence), [a,g,-][-] (a gap in the protein sequence and a codon with an insert at pos 3) and so on. Damn those null sub-spaces and all their spawn. Matthew --- Keith James <[EMAIL PROTECTED]> wrote: > > Following up my own post, but anyway... I've made > the MotifTools test > pass again. However in trying to eliminate the gap > character (which > I'm still not sure I should be doing) I tried to > test for the gap > symbol in DNA using mySymbol == > AlphabetManager.getGapSymbol() but > this didn't work (didn't return true for the DNA > gap). > > Stringifying the DNA gap object I get > > org.biojava.bio.symbol.SimpleBasisSymbol: [] > > Can someone clarify the circumstances under which > the various gap > Symbol(s) are equal (or ==) to each other? > > ta, > Keith > > -- > > - Keith James <[EMAIL PROTECTED]> bioinformatics > programming support - > - Pathogen Sequencing Unit, The Wellcome Trust > Sanger Institute, UK - > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
