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 <[email protected]> wrote: > I can't figure out how to create a Profile object from a MSA file (e.g., > .msf) in biojava3. Any suggestions? > -- > Dave > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://mailman.open-bio.org/mailman/listinfo/biojava-l >
_______________________________________________ Biojava-l mailing list - [email protected] http://mailman.open-bio.org/mailman/listinfo/biojava-l
