[Biojava-dev] FW: Suffix tree

[Matthew Pocock]

Hi François,

The suffix tree impl is my fault. I wrote it as a
quick-and-dirty way to do kernel methods (like support
vector machines) over sequences. Since you have
working code, the best plan is probably for you to add
it to biojava as a seperate class, and then we can
work out how to provide both implementations to people
without twice the API.

Have you replaced SuffixTree with your code, or is it
a totaly seperate implementation?

Anyway, send code and get added to the biojava 1.3
authors list.

Matthew

 --- Francois Pepin <francois.pepin@mail.mcgill.ca>
wrote: > Hi everyone,
> 
> Is there anyone planning on doing a new version of
> the SuffixTree? Is
> there a reason I shouldn't go and do it myself?
> 
> I've got a pretty good implementation of Ukkonen's
> suffix tree algorithm
> that I shouldn't need to modify all that much to fit
> the current
> methods, and it should make it a lot faster for the
> tree creation
> (O(n)). It's also got a lot more features than the
> current one (since I
> needed it to do some ).
> 
> Or would it be better to just have it subclass it
> and override
> everything and then people can see what it's worth?
> 
> François Pepin
> 
> 
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> biojava-dev mailing list
> biojava-dev@biojava.org
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