RE: [Bioclipse-devel] BiojavaResource

[Emig, R. <Rob...@pi...>]

I'm a big fan of the way MOE and Mesquite load files

Allow user to open ANY file
Then go to another dialog to actually parse it

Text version of parse dialog....
We can use the biojava stuff to guess the file, and then read in....
------------------------------------------------------------
- File Data:          | Open file as...   | Example format
-                     | Sequence: Fasta   | >sequencename annotations
- >sequence blah blah | Sequence: MSF     | sequence
- ATGAMGIALMD         | Alignment: MSF    | sequence
- KLKLKLKPRLKTLK      | Sequence: Genbank |
-                     | Recommend: Sequence:Fasta |
------------------------------------------------------------

-Robin

-----Original Message-----
From: bio...@li...
[mailto:bio...@li...] On Behalf Of Egon
Willighagen
Sent: Sunday, March 26, 2006 9:33 PM
To: bio...@li...
Subject: Re: [Bioclipse-devel] BiojavaResource

On Sunday 26 March 2006 21:36, Mark Southern wrote:
> I propose that we use org.biojava.bio.seq.io.SeqIOTools to guess the
> type of sequence file and autoload it. Something like:

CDK uses such an algorithm for chem files too.

> The guessFileType() method IS deprecated in biojava but in many years
of
> using it, it has not failed me.=20

You could set up a number of test cases.

> In a gui application such as bioclipse=20
> it makes sense to try to best deal with what ever the user throws at
> you!

Egon

--=20
eg...@us...
Blog: http://chem-bla-ics.blogspot.com/
GPG: 1024D/D6336BA6


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