Hi all.
I've finally gotten back to some coding (at least for the afternoon), and have merged Natasha's changes in to the current 2.8.x release series, and you should be able to now do Stockholm file IO from the current release build available from the website.
There are a few things that still may behave strangely, including the parsing of accessions from the files. There's also no support (as yet) for parsing the PDB cross references included in Pfam files into PDB ID entries in Jalview (Natasha - if you're up for that - take a look over at http://issues.jalview.org/browse/JAL-1265 - it's a pretty sparse issue at the moment, but its all related to the test code now in test/jalview/io/StockholmFileTest.java ).
Jim.