[Biojava-l] (no subject)

[Keith James]

Hope this is intelligible. We have system crash, loss of homedirs, NFS
failure... this on cmd line mail w no backspace.

Checked in searched changes as discussed - i.e. switch to string ID. Made
change to relevant method names on feedback from users. Old methods are 
deprecated. Not sure if this is best - maybe just rename them in place? As
this is an interface all implementations currently have both sets :(

This was quite large change - had to fix tests and all impls. Also docs. 
Some builder impls still need query sequence holder SequenceDb and also
SequenceDBInstallation as before because they annotate Features onto
the sequences. However, simplest builder is now free of this. It's used
probably 90% of the time, so this is good.

Not checked in yet, but succeeded in getting pure Java DocBook build
requiring only Xalan + Ant to work. It's now simple to set up for DocBook
novices - download styleshheet and DTD, get Xalan, change 2 paths in build.xml
(can't see how to avoid this yet) and type 'ant docbook'

Added docbook task to buiold.xml so that it integrates with API docs similar
to way Sun Java documentation + API docs fit together. Woo hoo!

K