bio 1.5.1 → 2.0.2

data/test/unit/bio/db/biosql/tc_biosql.rb

@@ -1,114 +0,0 @@
-# To change this template, choose Tools | Templates
-# and open the template in the editor.
-
-# loading helper routine for testing bioruby
-require 'pathname'
-load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
-                            'bioruby_test_helper.rb')).cleanpath.to_s
-
-# libraries needed for the tests
-require 'test/unit'
-require 'bio'
-
-module Bio
-  class TestBiosqlIO < Test::Unit::TestCase
-    def setup
-      @connection = Bio::SQL.establish_connection({'development'=>{'hostname'=>'localhost','database'=>"bioseq", 'adapter'=>"jdbcmysql", 'username'=>"febo", 'password'=>nil}},'development')
-      @str_genbank=<<END
-LOCUS       X64011                   756 bp    DNA     linear   BCT 26-SEP-2006
-DEFINITION  Listeria ivanovii sod gene for superoxide dismutase.
-ACCESSION   X64011 S78972
-VERSION     X64011.1  GI:44010
-KEYWORDS    sod gene; superoxide dismutase.
-SOURCE      Listeria ivanovii
-  ORGANISM  Listeria ivanovii
-            Bacteria; Firmicutes; Bacillales; Listeriaceae; Listeria.
-REFERENCE   1
-  AUTHORS   Haas,A. and Goebel,W.
-  TITLE     Cloning of a superoxide dismutase gene from Listeria ivanovii by
-            functional complementation in Escherichia coli and characterization
-            of the gene product
-  JOURNAL   Mol. Gen. Genet. 231 (2), 313-322 (1992)
-   PUBMED   1736100
-REFERENCE   2  (bases 1 to 756)
-  AUTHORS   Kreft,J.
-  TITLE     Direct Submission
-  JOURNAL   Submitted (21-APR-1992) J. Kreft, Institut f. Mikrobiologie,
-            Universitaet Wuerzburg, Biozentrum Am Hubland, 8700 Wuerzburg, FRG
-COMMENT     On Jun 23, 2005 this sequence version replaced gi:244394.
-FEATURES             Location/Qualifiers
-     source          1..756
-                     /organism="Listeria ivanovii"
-                     /mol_type="genomic DNA"
-                     /strain="ATCC 19119"
-                     /db_xref="taxon:1638"
-     gene            95..746
-                     /gene="sod"
-     RBS             95..100
-                     /gene="sod"
-     CDS             109..717
-                     /gene="sod"
-                     /EC_number="1.15.1.1"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="superoxide dismutase"
-                     /protein_id="CAA45406.1"
-                     /db_xref="GI:44011"
-                     /db_xref="GOA:P28763"
-                     /db_xref="InterPro:IPR001189"
-                     /db_xref="UniProtKB/Swiss-Prot:P28763"
-                     /translation="MTYELPKLPYTYDALEPNFDKETMEIHYTKHHNIYVTKLNEAVS
-                     GHAELASKPGEELVANLDSVPEEIRGAVRNHGGGHANHTLFWSSLSPNGGGAPTGNLK
-                     AAIESEFGTFDEFKEKFNAAAAARFGSGWAWLVVNNGKLEIVSTANQDSPLSEGKTPV
-                     LGLDVWEHAYYLKFQNRRPEYIDTFWNVINWDERNKRFDAAK"
-     terminator      723..746
-                     /gene="sod"
-ORIGIN
-        1 cgttatttaa ggtgttacat agttctatgg aaatagggtc tatacctttc gccttacaat
-       61 gtaatttctt ttcacataaa taataaacaa tccgaggagg aatttttaat gacttacgaa
-      121 ttaccaaaat taccttatac ttatgatgct ttggagccga attttgataa agaaacaatg
-      181 gaaattcact atacaaagca ccacaatatt tatgtaacaa aactaaatga agcagtctca
-      241 ggacacgcag aacttgcaag taaacctggg gaagaattag ttgctaatct agatagcgtt
-      301 cctgaagaaa ttcgtggcgc agtacgtaac cacggtggtg gacatgctaa ccatacttta
-      361 ttctggtcta gtcttagccc aaatggtggt ggtgctccaa ctggtaactt aaaagcagca
-      421 atcgaaagcg aattcggcac atttgatgaa ttcaaagaaa aattcaatgc ggcagctgcg
-      481 gctcgttttg gttcaggatg ggcatggcta gtagtgaaca atggtaaact agaaattgtt
-      541 tccactgcta accaagattc tccacttagc gaaggtaaaa ctccagttct tggcttagat
-      601 gtttgggaac atgcttatta tcttaaattc caaaaccgtc gtcctgaata cattgacaca
-      661 ttttggaatg taattaactg ggatgaacga aataaacgct ttgacgcagc aaaataatta
-      721 tcgaaaggct cacttaggtg ggtcttttta tttcta
-//
-END
-    end
-
-    def test_00_connection
-      assert_instance_of(ActiveRecord::ConnectionAdapters::ConnectionPool, @connection)
-    end
-
-    def test_01_input_is_genbank
-      assert_instance_of(Bio::GenBank,Bio::GenBank.new(@str_genbank))
-    end
-
-    def test_02_insert_bioentry
-      @@x = Bio::SQL::Sequence.new(:biosequence=>Bio::GenBank.new(@str_genbank).to_biosequence, :biodatabase=>Bio::SQL::Biodatabase.find(:first))
-      assert_not_nil(@@x)
-    end
-
-    def test_03_input_output
-      bioseq = Bio::SQL.fetch_accession("X64011")
-      assert_not_nil bioseq
-      assert_equal(@str_genbank, bioseq.to_biosequence.output(:genbank))
-    end
-
-    def test_04_bioentry_data_format
-      assert_equal('26-SEP-2006', @@x.date_modified.to_s)
-    end
-
-    def test_05_title
-      assert_equal('Cloning of a superoxide dismutase gene from Listeria ivanovii by functional complementation in Escherichia coli and characterization of the gene product',@@x.references.first.title)
-    end
-    def test_99_delete_bioentry
-      assert_not_nil(@@x.delete)
-    end
-  end
-end

data/test/unit/bio/db/biosql/ts_suite_biosql.rb

@@ -1,8 +0,0 @@
-# To change this template, choose Tools | Templates
-# and open the template in the editor.
-$:.unshift File.dirname(__FILE__)
-
-require 'test/unit' 
-
-# Add your testcases here
-require 'tc_biosql'

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

@@ -1,821 +0,0 @@
-#
-# = 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)
-      phyloxml.close
-    end
-
-    def test_open_with_block
-      filename = TestPhyloXMLData.example_xml
-      phyloxml_bak = nil
-      ret = Bio::PhyloXML::Parser.open(filename) do |phyloxml|
-        assert_instance_of(Bio::PhyloXML::Parser, phyloxml)
-        common_test_next_tree(phyloxml)
-        phyloxml_bak = phyloxml
-        "ok"
-      end
-      assert_equal("ok", ret)
-      assert_equal(true, phyloxml_bak.closed?)
-    end
-
-    def test_new
-      str = File.open(TestPhyloXMLData.example_xml, "rb") { |f| f.read }
-      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(&block)
-      Bio::PhyloXML::Parser.open(TestPhyloXMLData.example_xml, &block)
-    end
-    private :phyloxml_open
-
-    def test_close
-      phyloxml = phyloxml_open
-      phyloxml.next_tree
-      assert_nil(phyloxml.close)
-    end
-
-    def test_closed?
-      phyloxml = phyloxml_open
-      assert_equal(false, phyloxml.closed?)
-      phyloxml.next_tree
-      assert_equal(false, phyloxml.closed?)
-      phyloxml.close
-      assert_equal(true, phyloxml.closed?)
-    end
-
-    def test_closed_with_block
-      ret = phyloxml_open do |phyloxml|
-        assert_equal(false, phyloxml.closed?)
-        phyloxml.next_tree
-        assert_equal(false, phyloxml.closed?)
-        phyloxml
-      end
-      assert_equal(true, ret.closed?)
-    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_next_tree_after_open_with_block
-      phyloxml = phyloxml_open { |arg| arg }
-      assert_raise(LibXML::XML::Error) { phyloxml.next_tree }
-    end
-
-    def test_close_after_open_with_block
-      phyloxml = phyloxml_open { |arg| arg }
-      assert_raise(LibXML::XML::Error) { phyloxml.close }
-    end
-
-    def test_close_in_open_with_block
-      phyloxml = phyloxml_open do |arg|
-        ret = arg
-        assert_nil(arg.close)
-        ret
-      end
-      assert_raise(LibXML::XML::Error) { phyloxml.close }
-    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