I was wondering if anyone has successfully gotten
BlastXMLParserFacade to work on an xml style NCBI
blast output file (version 2.2.3)? I'm getting null
pointer exceptions deep within the crimson parser
implementation classes, but I now i'm correctly
passing in the NCBI output file, since the dtd is
Hi all. I'm trying to optimize the transition states probabilities for my
HMM. I already have set them to values which I think are pretty good.
Since I know the Baum Welch can only help with the scores and optimize
them up to a local maxima I thought of using the parameters I calculated
as a starti
Hi Stephane -
Within EmissionState you can set a Distribution that contains emission
probabilities for the Symbols states emission alphabet using the
setDistribution method. This Distribution will be your predetermined
weights.
To set the transition probabilities you can use the setWeights(Sta
> Hi Stephane -
>
> Within EmissionState you can set a Distribution that contains emission
> probabilities for the Symbols states emission alphabet using the
> setDistribution method. This Distribution will be your predetermined
> weights.
>
> To set the transition probabilities you can use the set
Sorry for the previous error.
Original Message
Subject: Re: [Biojava-l] Parameter Settings in BaumWelchTraining
From:[EMAIL PROTECTED]
Date:Fri, March 12, 2004 12:27 am
To: [EMAIL PROTECTED]
-
When you call the train() method of the BaumWelchTrainer you supply it
with a SequenceDB. The sequences from this DB are used to optimize the
weights of the model.
However, I have a bad feeling that when you train your model with the
BaumWelchTrainer your previously set counts will be ignored a
