--- Jan W�rthner <[EMAIL PROTECTED]> wrote: > > Hi, > > does anyone know, if there is a biojava way to > construct a Sequence object by > reading sequence data from an XML file?
Hi Jan, Asking if we have parsers for XML is a bit like asking if we have parsers for ASCII - there are loads of ways to encode the same data with XML. We currently support (to a greater or lesser extent) game, agave, das-xml and XFF. > > I store all the information in XML files (e.g. > connecting via > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=text&db=Nucleotide&dopt=XML&uid=1234). OK - reading this now. It looks like a semi-sane XML version of genbank/embl. You should fairly easily be able to write a sax or stax handler for this that calls methods on a SeqIOListener. > I know that SeqIOTools offers methods for reading > sequences from files > (fileToBioJava()), but unfortunately XML is not > among the supported formats. What do you do at the moment? Do you have your own parsers, or do you use somebody elses? > > kind regards > Jan W�rthner Matthew ________________________________________________________________________ Want to chat instantly with your online friends? Get the FREE Yahoo! Messenger http://mail.messenger.yahoo.co.uk _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
