[Biojava-dev] KMP matcher

[Matthew Pocock]

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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