[Biojava-dev] KMP matcher

[Schreiber, Mark]

I have committed this class to org.biojava.bio.search on the cvs trunk
only. This seemed to be the best place for it although I have to admit
I'm not too familiar with the search API so if someone wants to modify
it so that does fancy event driven stuff or fits better with the rest of
the API be my guest.

- Mark


> -----Original Message-----
> From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] 
> Sent: Thursday, 22 August 2002 11:26 a.m.
> To: Schreiber, Mark
> Cc: Biojava-dev@biojava.org
> Subject: Re: [Biojava-dev] KMP matcher
> 
> 
> Schreiber, Mark wrote:
> > Hi -
> > 
> > I have written (almost, minor debugging to go) an implementation of 
> > the Knuth-Moore-Pratt algorithm for rapidly finding exact 
> substrings 
> > in a String. Actually I've biojava'd it to find sub sequences in a 
> > sequence. Could be useful for the restriction enzyme search 
> problem or 
> > finding the location of probes in large sequences.
> > 
> > Anyhow my question is, in which package does it belong?
> > 
> > - Mark
> 
> Presumably it will return some collection or stream of hits? 
> This sounds 
> like it would match the search interfaces in 
> org.biojava.bio.search, or 
> org.biojava.bio.program.ssaha.HitListener even. I don't realy 
> have much 
> of an idea where to put it though - somewhere under 
> org.biojava.bio I guess.
> 
> Matthew
> 
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