[Biojava-l] Artemis as DAS client

[Keith James]

I've got Artemis to accept data from the Ensembl DAS reference server
and the whole thing has lurched into life like some sort of nameless
undead abomination from an H. P. Lovecraft novel.

As there are some holes in the DAS feature implementations (e.g. can't
make templates, null pointer exceptions when I use them as hash keys
etc.) I'll wait until the code stabilises a bit.

One this I've noticed is that the sub features (e.g. transcripts) seem
to be arriving on a different coordinate system. The coodinates
appearing in Artemis are the same as described for the transcript on
the Ensembl web site. I can't find documantation on the various
coordinate systems on the Ensembl site.

Are the transcript coordinates contig-centric? I can't find the
relationship between FPC contigs / static_golden_path contigs and the
chromosome, which is one way I could shift the coodinates back
(because I have asked Artemis to show a subsection based on chromosome
coordinates).

thanks,

-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA