From fe4e20b383203a7bba5f20f836076688165e0e9d Mon Sep 17 00:00:00 2001
From: "cmzmasek@gmail.com"
 <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Tue, 1 Mar 2011 03:49:20 +0000
Subject: [PATCH] Edited wiki page PhyloBioRuby through web user interface.

---
 wiki/PhyloBioRuby.wiki |   56 +++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 51 insertions(+), 5 deletions(-)

diff --git a/wiki/PhyloBioRuby.wiki b/wiki/PhyloBioRuby.wiki
index 70ed776..e7cfbd3 100644
--- a/wiki/PhyloBioRuby.wiki
+++ b/wiki/PhyloBioRuby.wiki
@@ -189,13 +189,17 @@ require 'bio'
 
 = Phylogenetic Trees =
 
+
 == Phylogenetic Tree Input and Output ==
 
+
 === Reading in of Phylogenetic Trees ===
 
-_... to be done_
 
-====Newick or New Hamphshire Format====
+
+====Newick or New Hampshire Format====
+
+_... to be done_
 
 {{{
 #!/usr/bin/env ruby
@@ -207,18 +211,35 @@ require 'bio'
 
 Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].
 
+In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command: 
+
+{{{
+% gem install -r libxml-ruby
+}}}
+
 {{{
 #!/usr/bin/env ruby
 require 'bio'
 
-}}}
+# This creates new phyloXML parser.
+phyloxml = Bio::PhyloXML::Parser.new('example.xml')
+
+# This prints the names of all trees in the file.
+phyloxml.each do |tree|
+  puts tree.name
+end
 
-Also, see: 
+# If there are several trees in the file, you can access the one you wish via index.
+tree = phyloxml[3]
+
+}}}
 
 
 
 === Writing of Phylogenetic Trees ===
 
+====Newick or New Hampshire Format====
+
 _... to be done_
 
 {{{
@@ -227,7 +248,32 @@ require 'bio'
 
 }}}
 
-Also, see: https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation
+====phyloXML Format====
+
+Partially copied from [https://www.nescent.org/wg_phyloinformatics/BioRuby_PhyloXML_HowTo_documentation Diana Jaunzeikare's documentation].
+
+In addition to !BioRuby, a libxml Ruby binding is also required. This can be installed with the following command: 
+
+{{{
+% gem install -r libxml-ruby
+}}}
+
+
+{{{
+#!/usr/bin/env ruby
+require 'bio'
+
+# this creates new phyloXML writer.
+writer = Bio::PhyloXML::Writer.new('tree.xml')
+
+# Writes tree to the file "tree.xml".
+writer.write(tree1)
+
+# Adds another tree to the file.
+writer.write(tree2)
+
+
+}}}
 
 
 
-- 
1.7.10.2