[Biojava-dev] Fixes fro Genpept writing

[Schreiber, Mark]

Hi -

I could tentatively volunteer to be tzar (until I am replaced by a
popular revolution!).

Some basic rules might be useful:

1) If you commit to biojava-live and not biojava1.3 branch then you
should tell me.
Is it possible to set up a notification system that sends a message
(preferably a daily digest) of stuff that has changed in the
biojava-live system (and the biojava 1.3 branch)?


2) No breaking the 1.3 api. No exceptions. If you want breakage let it
go into 1.4

3) No new APIs. Bug fixes and minor additional functionality are OK.

4) Try using JavaDoc sometime you'll like it :)

5) Must pass Junit tests (and preferably provide one if there isn't one
currently).

OK, 5 edicts is enough for someone who hasn't even scored a popular vote
yet :)

- Mark


-----Original Message-----
From: Matthew Pocock [mailto:matthew_pocock at yahoo.co.uk] 
Sent: Monday, 11 August 2003 5:42 a.m.
To: Schreiber, Mark
Subject: RE: [Biojava-dev] Fixes fro Genpept writing


IMHO it is desirable to port these things back, but do
we have the will? The options for porting when we have
things that should be ported seem to me to be one of

1) person who fixes it should port it

2) one person is "1.3 release tzar" - all patches go
through them

3) port patches when someone using the 1.3 series
complains or as/when we get embarased

If somebody want's to stand forward and be counted as
the release tzar, then great. Otherwise, I think we
should solomly swear to follow the port by patcher
principle. Any way you slice it, it means more work
though.

Matthew

 --- "Schreiber, Mark"
<mark.schreiber at agresearch.co.nz> wrote: > 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
> 	
> 	
> 	_______________________________________________
> 	biojava-dev mailing list
> 	biojava-dev at biojava.org
> 	http://biojava.org/mailman/listinfo/biojava-dev
> 	
> 
> 
>
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