[Biojava-dev] Fixes fro Genpept writing

[Schreiber, Mark]

Should we be activley porting this stuff back to the 1.3 branch?

	-----Original Message----- 
	From: David Huen [mailto:smh1008 at cus.cam.ac.uk] 
	Sent: Sun 10/08/2003 8:21 a.m. 
	To: biojava-dev at biojava.org 
	Cc: 
	Subject: [Biojava-dev] Fixes fro Genpept writing
	
	

	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
	
	
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