[Biojava-l] Need help in my code

[erw wer]

Hi, 

I am a beginner in biojava as well bioinformatics. I
hope you can advice on the obstacles I am facing now. 

I am trying to follow your example about the profile
HMM at
http://www.biojava.org/docs/bj_in_anger/profileHMM.htm,
and I try to fill in those missing codes that are
required. And finally I got it running. 

The code has no problem running until
BaumWelchTrainer.

But there is an exception when I try to score the
sequence and outputting the state path. I am not sure
if the way I code the test sequence initialization is
correct:
------------------------------------------------------
StatePath obs_rolls      = dp.generate(18);
SymbolList roll_sequence =
obs_rolls.symbolListForLabel(StatePath.SEQUENCE);
SymbolList[] sla         = {roll_sequence};
------------------------------------------------------
The exception says "Symbol d-1 not found in alphabet
Transitions from d-1", which is at dp.generate(18).

I appreciate if you can help me look into it. The
source code & the input file is attached for your ref.

And, what is dp.generate(int) means? If I have a
number of variable length sequences, should I take the
longest length of those sequences? or I am wrong
totally about what it means? 

THANKS!!


__________________________________
Do you Yahoo!?
The New Yahoo! Shopping - with improved product search
http://shopping.yahoo.com
-------------- next part --------------
>SEQ0
FPHFDLSHGSAQ

>SEQ1
FESFGDLSTPDAVMGNPK

>SEQ2
FDRFKHLKTEAEMKASED

>SEQ3
FTQFAGKDLESIKGTAP

>SEQ4
FPKFKGLTTADQLKKSAD

>SEQ5
FSFLKGTSEVPQNNPE

>SEQ6
FGFSGASDPG
-------------- next part --------------
A non-text attachment was scrubbed...
Name: PHMM.java
Type: application/octet-stream
Size: 4297 bytes
Desc: PHMM.java
Url : http://portal.open-bio.org/pipermail/biojava-l/attachments/20031013/a365e0ef/PHMM.obj