[Biojava-l] create Profile from a file in biojava3

[Michael Heuer]

Hello Dave,

>From what I can tell from the biojava3-alignment API

http://www.biojava.org/docs/api/org/biojava3/alignment/package-summary.html

and the detailed notes from Mark Chapman's GSoC MSA project

http://biojava.org/wiki/GSoC:MSA

I don't think you can read in an existing MSA from a file into the biojava3
Profile class.  You could just perform the MSA with biojava3

http://biojava.org/wiki/BioJava:CookBook3:MSA


Alternatively, in biojava-legacy there is a clustalw parser

http://www.biojava.org/docs/api1.9.1/org/biojava/bio/program/sax/ClustalWAlignmentSAXParser.html

I've never used that package though and don't know how well it has kept up
with changes to clustalw if at all.

   michael




On Sat, Dec 20, 2014 at 3:41 PM, Dave Roe <daveroe25 at gmail.com> wrote:

> I can't figure out how to create a Profile object from a MSA file (e.g.,
> .msf) in biojava3. Any suggestions?
> --
> Dave
>
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