[Biojava-l] Stop condition for blast parser

[Marcel Huntemann]

Hi Mark!

Mark Schreiber wrote:
> You could just customize BlastEcho to pass on the events of interest,
> ignore those that are not interesting. 
That's what I am doing right now. But I don't know, how to tell my
customized BlastEcho to stop, when a certain condition is met during a
paricular event call. What's the command for stopping there?

> It could also exit if a certain
> event occurs.
How?

> Remember it cost almost nothing to read the file so you
> save time by only sending interesting events for parsing.
Hmm, I am not sure, if it's really almost nothing, when I've about 90,000
contigs that were blasted against a database with about maybe 3,000,000
genes. The blast output that I am parsing is about 13Gig big and every
cycle I am looking for the results of one particular contig of these
90,000 contigs. So I definitely experienced that the time sums up a lot,
when it's running in each of these 90,000 cycles over the whole file,
although the contig I am looking for was already at the beginning of the file.


Cheers,
Marcel

> 
>     On 7 Mar 2009, 12:01 PM, "Marcel Huntemann"
>     <marcel.huntemann at gmail.com <mailto:marcel.huntemann at gmail.com>> wrote:
> 
>     But where? I can't do it in my customized handler, can I?
> 
>     Mark Schreiber wrote: > Because the blast parser uses event based
>     parsing you should be able to > c...
> 
>     > <marcel.huntemann at gmail.com <mailto:marcel.huntemann at gmail.com>
>     <mailto:marcel.huntemann at gmail.com
>     <mailto:marcel.huntemann at gmail.com>>> wrote: > > Hi! > > ...
> 
>     >     <mailto:Biojava-l at lists.open-bio.org
>     <mailto:Biojava-l at lists.open-bio.org>>
> 
>     > http://lists.open-bio.org/mailman/listinfo/biojava-l >
>