<div dir="ltr"><div><div><div><div>Hello Dave,<br><br></div>From what I can tell from the biojava3-alignment API<br><br><a href="http://www.biojava.org/docs/api/org/biojava3/alignment/package-summary.html">http://www.biojava.org/docs/api/org/biojava3/alignment/package-summary.html</a><br><br>and the detailed notes from Mark Chapman's GSoC MSA project<br><br><a href="http://biojava.org/wiki/GSoC:MSA">http://biojava.org/wiki/GSoC:MSA</a><br><br>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<br><br><a href="http://biojava.org/wiki/BioJava:CookBook3:MSA">http://biojava.org/wiki/BioJava:CookBook3:MSA</a><br><br><br></div>Alternatively, in biojava-legacy there is a clustalw parser<br><br><a href="http://www.biojava.org/docs/api1.9.1/org/biojava/bio/program/sax/ClustalWAlignmentSAXParser.html">http://www.biojava.org/docs/api1.9.1/org/biojava/bio/program/sax/ClustalWAlignmentSAXParser.html</a><br><br></div>I've never used that package though and don't know how well it has kept up with changes to clustalw if at all.<br><br></div> michael<br><br><div><div><br><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Dec 20, 2014 at 3:41 PM, Dave Roe <span dir="ltr"><<a href="mailto:daveroe25@gmail.com" target="_blank">daveroe25@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I can't figure out how to create a Profile object from a MSA file (e.g., .msf) in biojava3. Any suggestions?<span class="HOEnZb"><font color="#888888"><br clear="all"><div><div><div><div dir="ltr"><div>-- <br></div>Dave<br></div></div></div>
</div></font></span></div>
<br>_______________________________________________<br>
Biojava-l mailing list - <a href="mailto:Biojava-l@mailman.open-bio.org">Biojava-l@mailman.open-bio.org</a><br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biojava-l" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-l</a><br></blockquote></div><br></div>