Following up my own post, but anyway... I've made the MotifTools test
pass again. However in trying to eliminate the gap character (which
I'm still not sure I should be doing) I tried to test for the gap
symbol in DNA using mySymbol == AlphabetManager.getGapSymbol() but
this didn't work (didn't re
Hi Keith,
You can simply call sym.getMatches().size() == 0, and
if true, it is a symbol with gaps. For all the cases
the regex stuff will be used for any time soon, this
is good enough.
Basicaly, two gaps are the same if they have the same
arrangement of nested [] in their toString(). This is
equ
--- Phillip Lord <[EMAIL PROTECTED]> wrote: >
> "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 assumi
On Mon, Dec 02, 2002 at 11:56:58AM -0500, Dudgeon, Tim wrote:
> 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 do
> "Matthew" == Matthew Pocock <[EMAIL PROTECTED]> writes:
>> GO allows multiple parents along both is-a, and part-of. In the
>> case of GO, there are only two relationship types, but some of
>> the GOBO ontologies define others. It wouldn't really make sense
>> to have an API supportin
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The results are in for the !!!Extreme Times!!! Site of the month as voted by you our
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Has anyone looked at the gene ontology (or any other bits) in Duke
University's DBSR java resources?
http://mendel.mc.duke.edu:1755/libraries/dbsr/index.html
The documentation is non-existant so not sure whats in their packages
exactly
Russell
___
Bioja
