bio 1.3.1 → 1.4.0

data/test/unit/bio/db/test_gff.rb

@@ -9,10 +9,12 @@
 #  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'digest/sha1'
 require 'bio/db/gff'

data/test/unit/bio/db/test_lasergene.rb

@@ -1,19 +1,21 @@
 #
-# test/unit/bio/db/test_rebase.rb - Unit test for Bio::Lasergene
+# test/unit/bio/db/test_lasergene.rb - Unit test for Bio::Lasergene
 #
 # Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
 # Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu)
 # License::   The Ruby License
 #
-#  $Id: test_lasergene.rb,v 1.2 2007/04/05 23:35:43 trevor Exp $
+#  $Id:$
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
-require 'bio'
+require 'bio/sequence'
 require 'bio/db/lasergene'
 
 module Bio #:nodoc:

data/test/unit/bio/db/test_medline.rb

@@ -5,10 +5,12 @@
 # License::    The Ruby License
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/db/medline'
 

data/test/unit/bio/db/test_newick.rb

@@ -6,16 +6,16 @@
 #               Naohisa Goto <ng@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: test_newick.rb,v 1.6 2007/12/12 16:06:22 ngoto Exp $
+# $Id:$
 #
 
-require 'test/unit'
-
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), [".."] * 4, "lib")).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
-require 'bio'
+# libraries needed for the tests
+require 'test/unit'
 require 'bio/tree'
 require 'bio/db/newick'
 

data/test/unit/bio/db/test_nexus.rb

@@ -12,10 +12,12 @@
 # This file contains unit tests for Bio::Nexus.
 #
 
+# loading helper routine for testing bioruby
 require 'pathname'
-libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
-$:.unshift(libpath) unless $:.include?(libpath)
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
 
+# libraries needed for the tests
 require 'test/unit'
 require 'bio/db/nexus'
 

data/test/unit/bio/db/test_phyloxml.rb

@@ -0,0 +1,769 @@
+#
+# = test/unit/bio/db/test_phyloxml.rb - Unit test for Bio::PhyloXML::Parser
+#
+# Copyright::   Copyright (C) 2009
+#               Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
+# License::     The Ruby License
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+
+begin
+  require 'libxml'
+rescue LoadError
+end
+
+if defined?(LibXML) then
+  require 'bio/db/phyloxml/phyloxml_parser'
+end
+
+module Bio
+  class TestPhyloXML_Check_LibXML < Test::Unit::TestCase
+    def test_libxml
+      assert(defined?(LibXML),
+             "Error: libxml-ruby library is not present. Please install libxml-ruby library. It is needed for Bio::PhyloXML module. Unit test for PhyloXML will not be performed.")
+    end
+  end #class TestPhyloXML_LibXMLCheck
+end #module Bio
+
+module Bio
+
+  module TestPhyloXMLData
+
+  PHYLOXML_TEST_DATA = Pathname.new(File.join(BioRubyTestDataPath, 'phyloxml')).cleanpath.to_s
+
+  def self.example_xml
+    File.join PHYLOXML_TEST_DATA, 'phyloxml_examples.xml'
+    #If you want to test the output of writer, then do this:
+    #File.join PHYLOXML_TEST_DATA, 'phyloxml_examples_test.xml'
+    # But make sure you run ruby test/unit/bio/db/test_phyloxml_writer.rb before
+  end
+
+  def self.made_up_xml
+    File.join PHYLOXML_TEST_DATA, 'made_up.xml'
+    #If you want to test the output of writer, then do this:
+    #File.join PHYLOXML_TEST_DATA, 'made_up_test.xml'
+    # But make sure you run ruby test/unit/bio/db/test_phyloxml_writer.rb before
+  end
+
+  def self.metazoa_xml
+    File.join PHYLOXML_TEST_DATA, 'ncbi_taxonomy_metazoa.xml'
+  end
+
+  def self.mollusca_xml
+    File.join PHYLOXML_TEST_DATA, 'ncbi_taxonomy_mollusca.xml'
+  end
+
+  def self.life_xml
+    File.join PHYLOXML_TEST_DATA, 'tol_life_on_earth_1.xml'
+  end
+
+  def self.dollo_xml
+    File.join PHYLOXML_TEST_DATA, 'o_tol_332_d_dollo.xml'
+  end
+
+  def self.mollusca_short_xml
+    File.join PHYLOXML_TEST_DATA, 'ncbi_taxonomy_mollusca_short.xml'
+  end
+
+end #end module TestPhyloXMLData
+
+  
+
+  class TestPhyloXML_class_methods < Test::Unit::TestCase
+  
+    def test_open
+      filename = TestPhyloXMLData.example_xml
+      assert_instance_of(Bio::PhyloXML::Parser,
+                         phyloxml = Bio::PhyloXML::Parser.open(filename))
+      common_test_next_tree(phyloxml)
+    end
+
+    def test_new
+      str = File.read(TestPhyloXMLData.example_xml)
+      assert_instance_of(Bio::PhyloXML::Parser,
+                         phyloxml = Bio::PhyloXML::Parser.new(str))
+      common_test_next_tree(phyloxml)
+    end
+
+    def test_for_io
+      io = File.open(TestPhyloXMLData.example_xml)
+      assert_instance_of(Bio::PhyloXML::Parser,
+                         phyloxml = Bio::PhyloXML::Parser.for_io(io))
+      common_test_next_tree(phyloxml)
+      io.close
+    end
+
+    def common_test_next_tree(phyloxml)
+      tree = phyloxml.next_tree
+      tree_arr = []
+      while tree != nil do
+        tree_arr[tree_arr.length] = tree.name
+        tree = phyloxml.next_tree
+      end      
+      assert_equal(13, tree_arr.length)
+    end
+    private :common_test_next_tree
+    
+  end #class TestPhyloXML_class_methods
+
+
+
+  class TestPhyloXML_private_methods < Test::Unit::TestCase
+    def setup
+      @phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLData.example_xml)
+    end
+
+    def teardown
+      @phyloxml.close
+    end
+
+    def test__validate
+      assert_nothing_raised {
+        @phyloxml.instance_eval {
+          _validate(:file, TestPhyloXMLData.example_xml)
+        }
+      }
+    end
+
+    def test__validate_string
+      assert_nothing_raised {
+        @phyloxml.instance_eval {
+          _validate(:string, '<?xml version="1.0"?><phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" xmlns="http://www.phyloxml.org"/>')
+        }
+      }
+    end
+
+    def test__validate_validation_error
+      libxml_set_handler_quiet
+      assert_raise(RuntimeError) {
+        @phyloxml.instance_eval {
+          _validate(:string, '<a>test</a>')
+        }
+      }
+      libxml_set_handler_verbose
+    end
+
+    def test__schema
+      s = @phyloxml.instance_eval { _schema }
+      assert_instance_of(LibXML::XML::Schema, s)
+    end
+
+    def test__secure_filename
+      assert_equal('http:/bioruby.org/test.xml',
+                   @phyloxml.instance_eval {
+                     _secure_filename('http://bioruby.org/test.xml')
+                   })
+    end
+
+    def test__secure_filename_unchanged
+      assert_equal('test/test.xml',
+                   @phyloxml.instance_eval {
+                     _secure_filename('test/test.xml')
+                   })
+    end
+
+    def test_ClosedPhyloXMLParser
+      cp = Bio::PhyloXML::Parser::ClosedPhyloXMLParser.new
+      assert_raise(LibXML::XML::Error) { cp.next_tree }
+    end
+
+    private
+
+    def libxml_set_handler_quiet
+      # Sets quiet handler.
+      # Note that there are no way to get current handler.
+      LibXML::XML::Error.set_handler(&LibXML::XML::Error::QUIET_HANDLER)
+    end
+
+    def libxml_set_handler_verbose
+      # Sets verbose handler (default LibXML error handler).
+      # Note that there are no way to get current handler.
+      LibXML::XML::Error.set_handler(&LibXML::XML::Error::VERBOSE_HANDLER)
+    end
+  end #class TestPhyloXML_private_methods
+
+
+
+  class TestPhyloXML_close < Test::Unit::TestCase
+    def phyloxml_open
+      Bio::PhyloXML::Parser.open(TestPhyloXMLData.example_xml)
+    end
+    private :phyloxml_open
+
+    def test_close
+      phyloxml = phyloxml_open
+      phyloxml.next_tree
+      assert_nil(phyloxml.close)
+    end
+
+    def test_close_after_close
+      phyloxml = phyloxml_open
+      phyloxml.close
+      assert_raise(LibXML::XML::Error) { phyloxml.close }
+    end
+
+    def test_next_tree_after_close
+      phyloxml = phyloxml_open
+      phyloxml.close
+      assert_raise(LibXML::XML::Error) { phyloxml.next_tree }
+    end
+
+    def test_close_does_not_affect_io
+      io = File.open(TestPhyloXMLData.example_xml)
+      phyloxml = Bio::PhyloXML::Parser.for_io(io)
+      phyloxml.next_tree
+      phyloxml.close
+      assert(!io.closed?)
+    end
+  end #class TestPhyloXML_close
+
+
+
+  class TestPhyloXML1 < Test::Unit::TestCase
+  
+    def setup
+      @phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLData.example_xml)
+    end
+
+    def teardown
+      @phyloxml.close
+    end
+    
+    def test_initialize
+      assert_instance_of(Bio::PhyloXML::Parser, @phyloxml)
+    end 
+      
+    def test_next_tree()
+      tree = @phyloxml.next_tree
+      tree_arr = []
+      while tree != nil do
+
+        tree_arr[tree_arr.length] = tree.name
+        tree = @phyloxml.next_tree
+      end      
+      assert_equal(13, tree_arr.length)
+    end
+     
+  end #class TestPhyloXML1
+
+
+
+  class TestPhyloXML2 < Test::Unit::TestCase
+  
+    #setup is called before and every time any function es executed.  
+    def setup
+      @phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLData.example_xml)
+      @tree = @phyloxml.next_tree
+    end
+    
+    def test_tree_name
+      assert_equal("example from Prof. Joe Felsenstein's book \"Inferring Phylogenies\"", @tree.name)
+    end
+    
+    def test_tree_description
+      assert_equal("phyloXML allows to use either a \"branch_length\" attribute or element to indicate branch lengths.", @tree.description)
+    end
+    
+    def test_branch_length_attribute
+      assert_equal(0.792, @tree.total_distance)
+    end
+
+    def test_rooted_atr
+       assert_equal(true, @tree.rooted)
+    end
+    
+   
+    def test_branch_length_tag
+      @tree = @phyloxml.next_tree
+      assert_equal(0.792, @tree.total_distance)
+    end
+    
+    def test_bootstrap
+      #iterate throuch first 2 trees to get to the third
+      @tree = @phyloxml.next_tree
+      @tree = @phyloxml.next_tree
+      node = @tree.get_node_by_name("AB")
+      assert_equal('bootstrap', node.confidences[0].type)
+      assert_equal(89, node.confidences[0].value)
+    end
+
+    def test_to_biotreenode_bootstrap
+      #iterate throuch first 2 trees to get to the third
+      @tree = @phyloxml.next_tree
+      @tree = @phyloxml.next_tree
+      node = @tree.get_node_by_name("AB")
+      bionode = node.to_biotreenode
+      assert_equal(89, bionode.bootstrap)
+    end
+
+    def test_duplications
+      4.times do
+        @tree = @phyloxml.next_tree
+      end
+      node = @tree.root
+      assert_equal(1, node.events.speciations)
+    end
+
+    def test_taxonomy_scientific_name
+      3.times do
+        @tree = @phyloxml.next_tree
+      end
+      t = @tree.get_node_by_name('A').taxonomies[0]
+      assert_equal('E. coli', t.scientific_name)
+      assert_equal("J. G. Cooper, 1863", t.authority)
+      t = @tree.get_node_by_name('C').taxonomies[0]
+      assert_equal('C. elegans', t.scientific_name)
+    end
+
+    def test_taxonomy_id
+      5.times do
+        @tree = @phyloxml.next_tree
+      end
+      leaves = @tree.leaves
+      codes = []
+      ids = []
+      #id_types = []
+      leaves.each { |node|
+        codes[codes.length] = node.taxonomies[0].code
+        ids[ids.length] = node.taxonomies[0].taxonomy_id
+        #id_types[id_types.length] = node.taxonomy.id_type
+      }
+      assert_equal(["CLOAB",  "DICDI", "OCTVU"], codes.sort)
+     #@todo assert ids, id_types. or create new class for id.
+    end
+
+    def test_taxonomy2
+      9.times do
+        @tree = @phyloxml.next_tree
+      end
+      taxonomy = @tree.root.taxonomies[0]
+      assert_equal("8556", taxonomy.taxonomy_id.value)
+      assert_equal("NCBI", taxonomy.taxonomy_id.provider)
+      assert_equal("Varanus", taxonomy.scientific_name)
+      assert_equal("genus", taxonomy.rank)
+      assert_equal("EMBL REPTILE DATABASE", taxonomy.uri.desc)
+      assert_equal("http://www.embl-heidelberg.de/~uetz/families/Varanidae.html", taxonomy.uri.uri)
+    end
+
+    def test_distribution_desc
+      9.times do
+        @tree = @phyloxml.next_tree
+      end
+      leaves = @tree.leaves
+      descrs = []
+      leaves.each { |node|
+        descrs << node.distributions[0].desc
+      }
+      assert_equal(['Africa', 'Asia', 'Australia'], descrs.sort)
+    end
+
+    def test_distribution_point
+      10.times do
+        @tree = @phyloxml.next_tree
+      end
+      point = @tree.get_node_by_name('A').distributions[0].points[0]
+      assert_equal("WGS84", point.geodetic_datum)
+      assert_equal(47.481277, point.lat)
+      assert_equal(8.769303, point.long)
+      assert_equal(472, point.alt)
+
+      point = @tree.get_node_by_name('B').distributions[0].points[0]
+      assert_equal("WGS84", point.geodetic_datum)
+      assert_equal(35.155904, point.lat)
+      assert_equal(136.915863, point.long)
+      assert_equal(10, point.alt)
+    end
+
+    def test_sequence
+      3.times do
+        @tree = @phyloxml.next_tree
+      end
+      sequence_a = @tree.get_node_by_name('A').sequences[0]
+      assert_equal('alcohol dehydrogenase', sequence_a.annotations[0].desc)
+      assert_equal("probability", sequence_a.annotations[0].confidence.type)
+      assert_equal(0.99, sequence_a.annotations[0].confidence.value)
+      sequence_b = @tree.get_node_by_name('B').sequences[0]
+      assert_equal('alcohol dehydrogenase', sequence_b.annotations[0].desc)
+      assert_equal("probability", sequence_b.annotations[0].confidence.type)
+      assert_equal(0.91, sequence_b.annotations[0].confidence.value)
+      sequence_c = @tree.get_node_by_name('C').sequences[0]
+      assert_equal('alcohol dehydrogenase', sequence_c.annotations[0].desc)
+      assert_equal("probability", sequence_c.annotations[0].confidence.type)
+      assert_equal(0.67, sequence_c.annotations[0].confidence.value)
+
+    end
+
+     def test_sequence2
+       4.times do
+         @tree = @phyloxml.next_tree
+       end
+       leaves = @tree.leaves
+       leaves.each { |node|
+         #just test one node for now
+         if node.sequences[0].id_source == 'x'
+           assert_equal('adhB', node.sequences[0].symbol)
+           assert_equal("ncbi", node.sequences[0].accession.source)
+           assert_equal('AAB80874', node.sequences[0].accession.value)
+           assert_equal('alcohol dehydrogenase', node.sequences[0].name)
+         end
+         if node.sequences[0].id_source == 'z'
+           assert_equal("InterPro:IPR002085",
+                        node.sequences[0].annotations[0].ref)
+         end
+       }
+     end
+
+     def test_sequence3
+       5.times do
+         @tree = @phyloxml.next_tree
+       end
+       @tree.leaves.each { |node|
+         if node.sequences[0].symbol == 'ADHX'
+          assert_equal('UniProtKB', node.sequences[0].accession.source)
+          assert_equal('P81431', node.sequences[0].accession.value)
+          assert_equal('Alcohol dehydrogenase class-3', node.sequences[0].name)
+          assert_equal(true, node.sequences[0].is_aligned)
+          assert_equal(true, node.sequences[0].is_aligned?)
+          assert_equal('TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD',
+                       node.sequences[0].mol_seq)
+          assert_equal('EC:1.1.1.1', node.sequences[0].annotations[0].ref)
+          assert_equal('GO:0004022', node.sequences[0].annotations[1].ref)
+         end
+       }
+     end
+
+     def test_to_biosequence
+       5.times do
+         @tree = @phyloxml.next_tree
+       end
+       @tree.leaves.each { |node|
+         if node.sequences[0].symbol =='ADHX'
+           seq = node.sequences[0].to_biosequence
+           assert_equal('Alcohol dehydrogenase class-3', seq.definition)
+           assert_equal('UniProtKB', seq.id_namespace)
+           assert_equal('P81431', seq.entry_id)
+           assert_equal('TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD',
+                        seq.seq.to_s)
+         end
+       }
+     end
+
+     def test_extract_biosequence
+       5.times do
+         @tree = @phyloxml.next_tree
+       end
+       @tree.leaves.each { |node|
+         if node.sequences[0].symbol == 'ADHX'
+           seq = node.extract_biosequence
+           assert_equal('Alcohol dehydrogenase class-3', seq.definition)
+           assert_equal('TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD',
+                        seq.seq.to_s)
+           assert_equal('Octopus vulgaris', seq.classification[0])
+         end
+       }
+     end
+
+     def test_date
+       11.times do
+         @tree = @phyloxml.next_tree
+       end
+       date_a = @tree.get_node_by_name('A').date
+       assert_equal('mya', date_a.unit)
+       assert_equal("Silurian", date_a.desc)
+       assert_equal(425, date_a.value)
+       date_b = @tree.get_node_by_name('B').date
+       assert_equal('mya', date_b.unit)
+       assert_equal("Devonian", date_b.desc)
+       assert_equal(320, date_b.value)
+       date_c = @tree.get_node_by_name('C').date
+       assert_equal('mya', date_c.unit)
+       assert_equal('Ediacaran', date_c.desc)
+       assert_equal(600, date_c.value)
+       assert_equal(570, date_c.minimum)
+       assert_equal(630, date_c.maximum)
+     end
+
+     def test_property
+       7.times do
+         @tree = @phyloxml.next_tree
+       end
+       property = @tree.get_node_by_name('A').properties[0]
+       assert_equal('xsd:integer', property.datatype)
+       assert_equal('NOAA:depth', property.ref)
+       assert_equal('clade', property.applies_to)
+       assert_equal('METRIC:m', property.unit)
+       assert_equal(' 1200 ', property.value)
+     end
+
+     def test_uri
+       9.times do
+         @tree = @phyloxml.next_tree
+       end
+       uri = @tree.root.taxonomies[0].uri
+       assert_equal("EMBL REPTILE DATABASE", uri.desc)
+       assert_equal("http://www.embl-heidelberg.de/~uetz/families/Varanidae.html", uri.uri)
+     end
+
+
+    
+  end #class TestPhyloXML2
+  
+  class TestPhyloXML3 < Test::Unit::TestCase
+  
+  TEST_STRING = 
+  """<phylogeny rooted=\"true\">
+      <name>same example, with support of type \"bootstrap\"</name>
+      <clade>
+         <clade branch_length=\"0.06\">
+            <name>AB</name>
+            <confidence type=\"bootstrap\">89</confidence>
+            <clade branch_length=\"0.102\">
+               <name>A</name>
+            </clade>
+            <clade branch_length=\"0.23\">
+               <name>B</name>
+            </clade>
+         </clade>
+         <clade branch_length=\"0.4\">
+            <name>C</name>
+         </clade>
+      </clade>
+   </phylogeny>"""
+   
+    def setup
+      phyloxml = Bio::PhyloXML::Parser.new(TEST_STRING)
+      @tree = phyloxml.next_tree()  
+
+    end
+  
+    def test_children
+      node =  @tree.get_node_by_name("AB")
+      # nodes  = @tree.children(node).sort { |a,b| a.name <=> b.name }
+      node_names = []
+      @tree.children(node).each { |children|
+        node_names[node_names.length] = children.name
+      }
+      node_names.sort!
+      assert_equal(["A", "B"], node_names)
+    end
+
+  
+  end # class
+
+  class TestPhyloXML4 < Test::Unit::TestCase
+
+    #test cases what pertain to tree
+
+    def test_clade_relation
+
+      @phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLData.example_xml)
+      7.times do
+        @tree = @phyloxml.next_tree
+      end
+       cr = @tree.clade_relations[0]
+       assert_equal("b", cr.id_ref_0)
+       assert_equal("c", cr.id_ref_1)
+       assert_equal("network_connection", cr.type)
+    end
+
+    def test_sequence_realations
+      @phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLData.example_xml)
+      5.times do
+        @tree = @phyloxml.next_tree
+      end
+
+      sr = @tree.sequence_relations[0]
+       
+       assert_equal("x", sr.id_ref_0)
+       assert_equal("y", sr.id_ref_1)
+       assert_equal("paralogy", sr.type)
+    end
+
+
+  end
+
+  class TestPhyloXML5 < Test::Unit::TestCase
+
+    #testing file made_up.xml
+    def setup
+      @phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLData.made_up_xml)
+    end
+
+    def test_phylogeny_confidence
+      tree = @phyloxml.next_tree()
+      assert_equal("bootstrap", tree.confidences[0].type)
+      assert_equal(89, tree.confidences[0].value)
+      assert_equal("probability", tree.confidences[1].type)
+      assert_equal(0.71, tree.confidences[1].value)
+    end
+
+    def test_to_biotreenode_probability
+      tree = @phyloxml.next_tree()
+      node = tree.get_node_by_name('c').to_biotreenode
+      assert_equal(nil, node.bootstrap)
+    end
+
+    def test_polygon
+      2.times do
+        @tree = @phyloxml.next_tree
+      end
+      polygon = @tree.get_node_by_name('A').distributions[0].polygons[0]
+      assert_equal(3, polygon.points.length)
+      assert_equal(47.481277, polygon.points[0].lat)
+      assert_equal("m", polygon.points[0].alt_unit)
+      assert_equal(136.915863, polygon.points[1].long)
+      assert_equal(452, polygon.points[2].alt)
+      polygon = @tree.get_node_by_name('A').distributions[0].polygons[1]
+      #making sure can read in second polygon
+      assert_equal(3, polygon.points.length)
+      assert_equal(40.481277, polygon.points[0].lat)
+    end
+
+    def test_reference
+      3.times do
+        @tree = @phyloxml.next_tree
+      end
+      references = @tree.get_node_by_name('A').references
+      assert_equal("10.1093/bioinformatics/btm619", references[0].doi)
+      assert_equal("Phyutility: a phyloinformatics tool for trees, alignments and molecular data", references[0].desc)
+      assert_equal("10.1186/1471-2105-9-S1-S23", references[1].doi)
+    end
+
+
+    def test_single_clade
+      4.times do
+        @tree = @phyloxml.next_tree()
+      end
+      assert_equal("A", @tree.root.name)
+    end
+
+    def test_domain_architecture
+      5.times {@tree = @phyloxml.next_tree()}
+      node = @tree.get_node_by_name("22_MOUSE")
+      assert_equal("22_MOUSE", node.name)
+      assert_equal("MOUSE", node.taxonomies[0].code)
+      domain_arch = node.sequences[0].domain_architecture
+      assert_equal(1249, domain_arch.length)
+      assert_equal(6, domain_arch.domains[0].from)
+      assert_equal(90, domain_arch.domains[0].to)
+      assert_in_delta(7.0E-26, domain_arch.domains[0].confidence, 1E-26)
+      assert_equal("CARD", domain_arch.domains[0].value)
+      assert_equal("x", domain_arch.domains[0].id)
+      assert_equal(733, domain_arch.domains[5].from)
+      assert_equal(771, domain_arch.domains[5].to)
+      assert_in_delta(4.7E-14, domain_arch.domains[5].confidence, 1E-15)
+      assert_equal("WD40", domain_arch.domains[5].value)
+      assert_equal(1168, domain_arch.domains.last.from)
+      assert_equal(1204, domain_arch.domains.last.to)
+      assert_equal(0.3, domain_arch.domains.last.confidence)
+      assert_equal("WD40", domain_arch.domains.last.value)
+    end
+
+    def test_clade_width
+      @tree = @phyloxml.next_tree
+      assert_equal(0.2, @tree.root.width)
+    end
+
+    def test_binary_characters
+      6.times do
+        @tree = @phyloxml.next_tree
+      end
+      bc =@tree.get_node_by_name("cellular_organisms").binary_characters
+      assert_equal("parsimony inferred", bc.bc_type)
+      assert_equal(0, bc.lost_count)
+      assert_equal(0, bc.gained_count)
+      assert_equal([], bc.lost)
+
+      bc2 = @tree.get_node_by_name("Eukaryota").binary_characters
+      assert_equal(2, bc2.gained_count)
+      assert_equal(["Cofilin_ADF", "Gelsolin"], bc2.gained)
+      assert_equal(["Cofilin_ADF", "Gelsolin"], bc2.present)
+    end
+
+    def test_rerootable2
+      6.times do
+        @tree = @phyloxml.next_tree
+      end
+      assert_equal(false, @tree.rerootable)
+    end
+
+    def test_phylogeny_attributes
+      @tree = @phyloxml.next_tree
+      assert_equal(true, @tree.rooted)
+      assert_equal(false, @tree.rerootable)
+      #@todo make this test pass
+      #assert_equal("1", @tree.branch_length_unit)
+
+    end
+
+    def test_taxonomy_synonym
+      5.times do
+        @tree = @phyloxml.next_tree
+      end
+      node = @tree.get_node_by_name('22_MOUSE')
+      t = node.taxonomies[0]
+      assert_equal("murine", t.synonyms[0])
+      assert_equal("vermin", t.synonyms[1])
+
+    end
+
+    def test_annotation_property
+      5.times do
+        @tree =@phyloxml.next_tree
+      end
+      node = @tree.get_node_by_name('22_MOUSE')
+      prop = node.sequences[0].annotations[0].properties[0]
+      assert_equal("1200", prop.value)
+    end
+
+  end
+  class TestPhyloXML5 < Test::Unit::TestCase
+
+    def test_each
+      phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLData.example_xml)
+      count = 0
+      phyloxml.each do |tree|
+        count +=1
+      end
+      assert_equal(13, count)
+    end
+
+    def test_other
+      phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLData.example_xml)
+      assert_equal(nil, phyloxml.other[0])
+      phyloxml.each do |tree|
+        #iterate through all trees, to get to the end
+      end
+      o = phyloxml.other[0]
+      assert_equal('align:alignment', o.element_name)
+      assert_equal('seq', o.children[0].element_name)
+      assert_equal('aggtcgcggcctgtggaagtcctctcct', o.children[1].value)
+      assert_equal("C", o.children[2].attributes["name"])
+
+    end
+
+    def test_array_behaviour
+      phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLData.example_xml)
+      tree = phyloxml[2]
+      assert_equal("same example, with support of type \"bootstrap\"",
+                   tree.name)
+    end
+
+
+#    def test_get_tree_by_name
+#       @phyloxml = Bio::PhyloXML::Parser.open(TestPhyloXMLData.made_up_xml)
+#       tree = @phyloxml.get_tree_by_name "testing confidence"
+#
+#    end
+
+  end
+
+
+end if defined?(LibXML) #end module Bio