> "Matthew" == Matthew Pocock <[EMAIL PROTECTED]> writes:
Matthew> Well spotted Sylvain, Keith, there's a method in
Matthew> AlphabetTools - getAllSymbols(). Feed it with the
Matthew> matches() map of the symbol & cat together the tokens
Matthew> from each of these.
I don't th
Would there be a reason why there is no "score" and "frame" field in the
Feature.template class? If they are not present in a Feature, then how
can they be outputted using a GFFWriter?
Stein.
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On Mon, Dec 02, 2002 at 10:44:27AM +, Keith James wrote:
>
> I don't think this method is behaving as expected. Passing the
> FiniteAlphabets from the following Symbols gets these results:
>
> a -> getMatches() -> getAllSymbols -> tokenize -> -a
> c -> getMatches() -> getAllSymbols -> tokeniz
> "Thomas" == Thomas Down <[EMAIL PROTECTED]> writes:
[...]
Thomas> It's fixed for now (see AlphabetManagerTest). If we ever
Thomas> re-write this code we *must* use some kind of globally
Thomas> unique names (URLs?) for Symbols and Alphabets, otherwise
Thomas> we'll end up
There has been mention of a Gene Ontology API and/or browser within BioJava
in the past.
I've also started off down that route, but before I go too far I thought it
made sense to check whether there was any consensus here.
I don't want to reinvent the wheel yet again and will be happy to help get
s
Research Associate
School of Computing Science, University of Newcastle, UK
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> "Tim" == Dudgeon, Tim <[EMAIL PROTECTED]> writes:
Tim> There has been mention of a Gene Ontology API and/or browser
Tim> within BioJava in the past. I've also started off down that
Tim> route, but before I go too far I thought it made sense to check
Tim> whether there was any consen
Hi Tim,
It's one of those things that would have been nice to
have a long time ago, but nobody ever wrote. What is
the API for a GO term? I'm wondering if we can just
re-use the Annotation/AnnotationType interfaces and
suck this in as a constrained Map.
Go terms have an ID and (possibly) a descr
> "Matthew" == Matthew Pocock <[EMAIL PROTECTED]> writes:
Matthew> Go terms have an ID and (possibly) a description. By the
Matthew> isa relationship, they have a (single?) parent and
Matthew> (possibly no) children. I'm assuming Go has a part-of
Matthew> relationship (or it's inverse,
