[Biojava-dev] GFFParser URL parsing problem

[Harmen van der Spek]

Hello,

I ran into a problem when using a GFF data source with Dazzle.
It contains an attribute href: which results in a link on a
DAS client, in our case Ensembl. The problem now is that attributes
are separated by semicolons, and the URLs contain semicolons too.
So the URL:
http://localhost/cgi-bin/gbrowse/dial_extra?name=Chr1;source=dial_extra;width=800;version=100;label=CGH

will be cut up in pieces and finally will not be rendered correctly.
Quoting the URL doesn't help.
Is this behaviour of parseAttribute in GFFParser.java intentional
or should this be considered as a bug, as quoting could be potentially
be used to distinguish between separators and URL semicolons.

Best regards,

Harmen