[Biojava-dev] ABI file parser

[Yan Bai]

Thank you all for helping me out.

Another question is about the ABI file parser, located in the package  org.biojava.bio.program.ABIFParser. Comments of this file indicate that it parses files from 377 DNA sequencer, while our sequence files are generated by 3730 XL,  are there any mismatches between these two formats? Is there a parser specific for 3730? I couldn't find anything describe the 3730 XL format like the one Clark Tibbett wrote.  

Thanks for any inputs.

Yan 

>>> "Dickson S. Guedes" <guedes at unisul.br> 03/22/06 2:01 PM >>>


Hi Yan,

Download BioJava
- http://biojava.org/wiki/BioJava:Download

Getting Started
- http://biojava.org/wiki/BioJava:GetStarted

Look at the sites above to get information about correct installation of 
Biojava framework.

[]s
-- 
Dickson S. Guedes
/*
  * UNISUL - Universidade do Sul de Santa Catarina
  * ATI - Assessoria de Tecnologia da Informação
  * (0xx48) 621-3200 - http://www.unisul.br
  *
  *    "Quis custodiet ipsos custodes?"
  */

Yan Bai wrotes:
 > I am new in this mailing list,
 > I've download biojava package, pretty sure CLASSPATH was set up 
right. I typed the example given on the tutorial (Trace2Seq.java), got 
compiler error as below. In biojava source code, I couldn't find the 
method named as "writeFasta" in SeqIOTools with "Sequence" as the 2nd 
parameter, neither did I find any methods with 'Sequence' as the 2nd 
parameter, but they all show up on API.
 > I am in the first step of trying Biojava, and this is frustrating. 
Apprecate if someone will help me out.
 > -------------------------------------
 > Trace2Seq.java:18: cannot find symbol
 > symbol  : method 
writeFasta(java.io.PrintStream,org.biojava.bio.seq.Sequence)
 > location: class org.biojava.bio.seq.io.SeqIOTools
 >       SeqIOTools.writeFasta(System.out, seq);
 >                 ^
 > 1 error
 > --------------------------------------