[Biojava-l] How to read a protein clustal alignment?
Mon, 1 Oct 2001 16:23:36 +0100
On Mon, Oct 01, 2001 at 12:15:37PM -0300, Damian D'Onia wrote:
> I'm trying to read a clustal file (.ALN) that contains protein
> sequences. Now I have a subclass of DefaultHandler which can read DNA
> sequences from .aln files, but I don't know how to fill a SymbolList from
> But, ProteinTools don't have a method like createDNA.
What version of BioJava are you using? Certainly, the current
CVS version has a method ProteinTools.createProtein(String), which
seems to do what you want.
However, it would seem cleaner to remove references to particular
alphabets from your code completely. You can do something like:
Alphabet alpha = DNATools.getDNA();
SymbolParser parser = alpha.getParser("token");
SymbolList sl = parser.parse(someString);
This is effectively what's happening inside DNATools.createDNA,
and means you can just parameterize your code with a particular
Hope this helps,