[Biojava-l] Re: format-filter

[Kim Rutherford]

On Fri, 21 Jan 2000 10:31:54 +0100, Christian Storm wrote:

> did anybody develop java-classes that can browse different database
> formats (EMBL, GenBank ,fasta ..) ? If not, anybody interested in doing
> so ? The idea would be to agree about an interface (or a abstract
> superclass) and to implement it for each format. I already wrote (like
> most of you, I guess) some database format filters, but I they lack a
> broad usability.

You might want to have look at the uk.ac.sanger.pathogens.embl package
distributed with Artemis.  It has classes that can read, write and
modify raw, FASTA, EMBL or GENBANK sequence files and complete EMBL and
GENBANK entries.


The javadoc documentation is here:

   http://www.sanger.ac.uk/Software/Artemis/artemis_docs/tree.html


The starting point if you want to read in a flat file is this class:

   http://www.sanger.ac.uk/Software/Artemis/artemis_docs/uk.ac.sanger.pathogens.embl.DocumentEntryFactory.html


An example of the package in action is here:

   ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/extra/TestEntry.java


Kim.