[Biojava-l] blast parsing and empty hits

Doug Rusch drusch@tcag.org
Thu, 3 Oct 2002 18:02:40 -0400

Point taken. I apologize if I offended anyone with my questions/comments, that was not my intent. I am very excited to be using BioJava and think that overall it is well designed. My initial instinct was to speak plainly but I freely admit that this is the first time I have participated in an open source project and I am not familiar with the open source etiquette.

I sincerely hope to begin contributing to the BioJava project in the near future. I want my changes to be as minimal as necessary so that the overall design is maintained, I want any changes I might introduce to be transparent (or as much so as possible) for already existing users, and I want to make sure the changes and the rational for them are well documented. 

Doug Rusch

-----Original Message-----
From:	Michael L. Heuer [mailto:heuermh@acm.org]
Sent:	Thu 10/3/2002 4:57 PM
To:	Doug Rusch
Cc:	biojava-l@biojava.org
Subject:	RE: [Biojava-l] blast parsing and empty hits

Hello Doug,

It's probably not best open source etiquette to put down the community
that you're trying to get help from.

Rather, you'd probably get a much warmer reception by providing patches
to the source files in question and junit test case(s) that exercise your


On Thu, 3 Oct 2002, Doug Rusch wrote:

> Actually I have made changes that fix both the no summary and "No hits
> found" problems though I have not done extensive testing and I do not
> know if this would work for wu-blast yet. Its more of a hack though than
> a nice solution. It would be nice to use the regex in 1.4 to put
> together a nice clear parser and I may do that in the near future. I am
> still surprised that this is even a problem. Is the community that small
> that obvious problems like this have not been fixed much earlier?
> Doug Rusch
> TCAG.org
> -----Original Message-----
> From:	Wiepert, Mathieu [mailto:Wiepert.Mathieu@mayo.edu]
> Sent:	Thu 10/3/2002 12:34 PM
> To:	Doug Rusch; Simon Brocklehurst
> Cc:	biojava-l@biojava.org
> Subject:	RE: [Biojava-l] blast parsing and empty hits
> Hi,
> I might add, that if you are familiar with java, and this is just one
> use case that fails, it would probably be easy enough to enhance the
> parser?  It may not be touched much because it works as is, sending off
> SAX events merrily.  At least I like to hope that is the case ;-)
> -Mat
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