[Biojava-dev] Fixes fro Genpept writing

[David Huen]

Following a bug report, I have checked and fixed a bug in SeqIOTools that
has prevented writing of Genpept files.  The bug comes about as a side
effect of switching the writeSequence method from the old deprecated 3
argument form to the the new 2 argument form.  It was no longer possible
thereby to specify a subformat type (Genpept vs Genbank) and the Genbank
formatter was erroneously applied to the Genpept data.

I have introduced a new GenpeptFormat object that inherits almost
entirely from GenbankFormat to handle Genpept data and patched the
SeqIOTool code to use this instead in writeGenpept().  If this is not the
current way we do this kind of thing then could someone more familiar with
the current form put in a better fix.

Interestingly, the code appears to have been broken for 5 months prior to
a complaint ;-)  Not much demand for Genpept file writing then.....

Regards,
David Huen