Hi,
I just wrote a homologene parser that includes unit tests. NCBI split
homologene into simple + complex file formats - I only parse the simple
format. Should I send you the code? I doubt you would want to
integrate it now, since I can imagine a few more useful methods, but,
with design pointers, I could extend the code to be more useful. Should
we take this discussion off the list?
Cheers,
Gary
[EMAIL PROTECTED] wrote:
Hello -
The best way to proove the code is worthy is to provide JUnit tests with
the code that provide good coverage of the functionality. If the tests
pass the code is worthy. Other more esoteric things like good API design
and efficiency are also nice but if the unit tests don't pass it doesn't
work.
Let us know what you plan to do.
- Mark
Gary Bader <[EMAIL PROTECTED]>
06/09/2005 05:53 AM
To: Mark Schreiber/GP/[EMAIL PROTECTED]
cc: biojava-l@biojava.org, [EMAIL PROTECTED]
Subject: Re: [Biojava-l] Homologene parser update?
Hi Mark,
Thanks. The changes that NCBI made to their file formats
are large, so
I could write another builder/parser for the new file format, but it
would not map completely to the existing parser (which is now broken
because of NCBI format changes to even the deprecated file format). If
I want to contribute code, who decides that the code is worthy (e.g.
does a design review)? Ideally, this would happen before I start coding.
I haven't figured out if I am going to use the existing
framework for
my current project, since the file format has become simpler, but I
would like to contribute if possible.
Thanks,
Gary
[EMAIL PROTECTED] wrote:
Hello -
It seems most of this was contributed by David Huen. I'm not sure if he
plans an update. If the changes are not large then you might want to
consider contributing the changes yourself.
Best of Luck
- Mark
Gary Bader <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
06/08/2005 08:22 AM
To: biojava-l@biojava.org
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] Homologene parser update?
Hi,
I just tried the Homologene parser in biojava 1.4pre1
and
noticed that
it only supports the deprecated Homologene file format and throws a
number of exceptions parsing that file (likely because of updates to the
old file format). Is there an update for this parser available
anywhere? I think it would be very useful.
Thanks,
Gary
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