ID	PROJECT	MEDIA_TYPE	HEADER	SENT_BY	REPLIES_TO	CONTENT	DATE	PARENT_MSG	THREAD_ID
1433	1	biojava-dev                                       	
 [Biojava-dev] Comments about OrderNDistributions
	58032	-1	
After going through the code for the OrderNDistributions, there are a
couple of comments and questions that I would have:
Is there any reason why the conditional probabilities instead of joint
probabilities are used there?
Right now, for OrderNDistribution.getWeight(cgt) (or any codon) gives
P(t.cg) while getting P(cgt) would be a lot more useful. It's quite easy
to go from the joint to the conditional probabilities while getting the
opposite information is pretty troublesome.
To get P(cgt), one would need to get P(t.cg).sum of P(g.nc).sum of
P(c.nn). (sum of P(g.nc).P(g.ac).P(g.cc).P(g.gc).P(g.tc) ).
I don't really see why not store it as joint probabilities and not have
to worry about the conditioning and conditioned alphabets there.
Also, I'm not positive about this, but it seems that some information
would be lost (or at least quite difficult to recover) about the first
few characters of the distribution, for example with AACCCGGG, it there
are no A's that would appear anywhere in a 3rd order (which would really
be a 2nd order Markov chain) distributions. Two ways of going around it
would be to carry all of the distributions of lower order to make sure
that you have the data around, but it's a bit cumbersome, or to have the
SymbolListViews.orderNSymbolList(AACCCGGG, 3) give out NNAACCCGGG in
this case, and have the orderNDistributions keep that into account.
What do people think about this?
Francois Pepin
	2003-03-03	-1	161890
1437	1	biojava-dev                                       	
 [Biojava-dev] biojava-acedb
	57986	58046	
Hi Matt,
I've just taken a look at the package. It doesn't
appear to have been touched for quite a while. I've
edited the Database interface (just removed the
commented out deffinition of fetch) and that portion
builds. The sequence binding package (org.acedb.seq)
doesn't build, but I've fixed a couple of the bit.rot
problems with it.
As I remember, the seq package was doomed to failure
from the start because every acedb instance uses
different and incompattible sequence and assembly
models. Also, at the time, we didn't have the
projection and assembly code working. If you do want
to make acedb look like a biojava SequenceDB, then I'd
be happy to help out where I can with words of
encouragement (or at least point you at the
appropreate bits of API).
Matthew
...."matthew couchman (JIC)."
wrote: . Hi, sorry if
you've already had this, my mail server
. seemed to be having problems...
. 
. I'm interested in using your extension to acedb but
. i'm having some problems compiling it from the
. distribution available through the site. It all
. seems to stem from Ace.java, line 97 which calls a
. method called fetch(AceURL) from a Database object.
. It seems that fetch(AceURL) isn't defined in the
. Database interface. Can you help?
. 
. Thanks very much,
. 
. Matt.
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