From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 24 Feb 2011 07:56:48 +0000 (+0000)
Subject: Edited wiki page PhyloBioRuby through web user interface.
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8ace8ed9c6cf72b4e3bfd613f2224c8d201ea040;p=jalview.git

Edited wiki page PhyloBioRuby through web user interface.
---

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index bfb1c4c..204edf0 100644
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -18,9 +18,19 @@ Tutorial for multiple sequence alignments and phylogenetic methods in BioRuby --
 {{{
 #!/usr/bin/env ruby
 require 'bio'
+
+# Calculates the alignment using the MAFFT program
+# on the local machine, and stores the result in 'report'.
 options = [ '--maxiterate', '1000', '--localpair' ]
-mafft = Bio::MAFFT.new('/home/zma/SOFTWARE/mafft-6.847-without-extensions/scripts/mafft', options )
+mafft = Bio::MAFFT.new('path/to/mafft', options )
 report = mafft.query_align( seqs)
+
+# Accesses the actual alignment
+align = report.alignment
+
+# Prints each sequence to the console.
+report.align.each { |s| puts s.to_s }
+#
 }}}