[Biojava-l] Problems with Annotations

2003-02-25 Thread Sylvain Foisy
Hi, I want to scan portions of sequences for motifs. I am trying to modify the annotation for the sequence so that each time a motif is found, I get a new annotation of the form "Motif x"+original annotation. It works when I print it on the terminal with System.out but when I try to save the seque

[Biojava-l] BioJava DAS Examples/Tutorial?

2003-02-25 Thread Ethan Cerami
Hi Everybody: Can anyone point me to any BioJava DAS examples / tutorials? I found the examples in the demos/das directory, but I was hoping for some more documentation. Any help is appreciated. Thanks, Ethan __ Do you Yahoo!? Yahoo! Tax Center

[Biojava-l] Relations between trainers

2003-02-25 Thread Oscar Lopes
Hi! I'm a graduate student and I'm using biojava to implement Viterbi training algorithm. I spent some time digging in the code, but I still can't make the relation between TrainigAlgorithm, DistributionTrainer, etc... What are the key classes that I can use? How does it work? I tried to look