The biojava LSID and the IBM LSID are slightly different APIs, the IBM one
the more complete of the two. There also are/were LSID client
implementations that I'm not very familiar with in taverna [0] and for
whatever reason in an email client called Haystack [1].
I would move the biojava LSID im
Hi
I need store some information from an ace assembly file(which is Phrap
plain text output). To do this I will have to write my own parses to
parse this complicated text file.
Is there any class In bioJava or anywhere else which does this.The best
scenario would be if some code converts thi
The internal use was mine (I was just using it as a substitute for a
namespace). Maybe we should upgrade it to be compatable with IBM or
Taverna?
- Mark
Michael Heuer <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
06/16/2005 03:27 AM
To: Gary Bader <[EMAIL PROTECTED]>
Hi -
The classes in org.biojava.bio.program.phred might do what you need
although they are more for reading phd files. They may give you a starting
point though.
- Mark
Avinash Kewalramani <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
06/16/2005 03:34 AM
To: biojava-l@bioja
Nope, nothing exists yet for reading Phrap/ACE. If you do end up writing
your own parser, it'd be really great if you could contribute it to the
project too.
The way the BioJava file parsers work removes the need for an
XML-translation step. File parsers read file, then fire events to
listeners, e
If your going to follow the event based parsing model (which I strongly
reccomend you do), I would make a Format implementation (possibly extended
if you need more methods) and fire your events at something like the
SimpleAssemblyBuilder object (again possibly extended if you need it to do
more
