bio-nexml 1.0.0 → 1.1.0

data/Rakefile

@@ -0,0 +1,36 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+# require 'rcov/rcovtask'
+# Rcov::RcovTask.new do |test|
+#   test.libs << 'test'
+#   test.pattern = 'test/**/test_*.rb'
+#   test.verbose = true
+# end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-nexml #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/TODO.txt

@@ -0,0 +1,6 @@
+* it would be good if objects could only be instantiated in the right nesting
+  order, e.g. you wouldn't do cell = Cell.new, but you'd do
+  cell = Row.create_cell and the nesting is automatically handled for you.
+  I think the way to do this is to require the containing object to be passed
+  (recursively) to the constructors, while create_foo internally does this,
+  passing self to the constructor.

data/VERSION

@@ -0,0 +1 @@
+1.0.0

data/bio-nexml.gemspec

@@ -0,0 +1,27 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  # meta
+  s.name        = 'bio-nexml'
+  s.version     = '1.1.0'
+  s.authors     = ['Rutger Vos', 'Anurag Priyam']
+  s.email       = ['rutgeraldo@gmail.com', 'anurag08priyam@gmail.com']
+  s.homepage    = 'https://github.com/nexml/bio-nexml'
+  s.license     = 'MIT'
+
+  s.summary     = %q{BioRuby plugin for reading and writing NeXML (http://nexml.org)}
+  s.description = %q{This plugin reads, writes and generates NeXML}
+
+  # dependencies
+  s.add_dependency('bio', '>= 1.4.1')
+  s.add_dependency('libxml-ruby', '= 1.1.4')
+
+  # gem
+  s.files         = `git ls-files`.split("\n") rescue ''
+  s.test_file     = "test/test_bio-nexml.rb"
+  s.require_paths = ["lib"]
+end
+

data/lib/bio/db/nexml.rb

@@ -1,10 +1,11 @@
-#load XML library for parser and serializer
 require 'xml'
+require 'bio/db/nexml/parser'
+require 'bio/db/nexml/writer'
+require 'bio/db/nexml/mapper'
+require 'bio/db/nexml/taxa'
+require 'bio/db/nexml/trees'
+require 'bio/db/nexml/matrix'
 
-#load required class and module definitions
-require "bio/db/nexml/mapper"
-
-#Autoload definition
 module Bio
   module NeXML
     
@@ -24,20 +25,6 @@ module Bio
       attr_accessor :xml_space
     end #end module Base
 
-    # Autoload multiple modules that reside in the same file.
-    def self.mautoload( modules, file )
-      modules.each do |m|
-        autoload m, file
-      end
-    end
-
-    mautoload %w|Otu Otus|,                                'bio/db/nexml/taxa.rb'
-    mautoload %w|Node Edge Tree Network Trees|,            'bio/db/nexml/trees.rb'
-    mautoload %w|State Char States Cell Sequence Format Characters|,  'bio/db/nexml/matrix.rb'
-
-    autoload :Parser, 'bio/db/nexml/parser'
-    autoload :Writer, 'bio/db/nexml/writer'
-
     class Nexml
       @@writer = Bio::NeXML::Writer.new      
       include Mapper

data/lib/bio/db/nexml/mapper/framework.rb

@@ -133,21 +133,18 @@ module Bio
           #    def each( &block )
           #      @targets.each( &block )
           #    end
-          class_eval <<_END_OF_EVAL_
-            def each_#{name}( &block )
-              repository( "#{target}", #{type} ).each( &block )
-            end
-_END_OF_EVAL_
+          define_method("each_#{name}") do |&block|
+            repository(target, type).each( &block )
+          end
 
           if type == HashRepository
             define_method( "get_#{name}_by_id" ) do |id,|
               repository( target, type )[ id ]          
             end                                        
-          class_eval <<_END_OF_EVAL_
-            def each_#{name}_with_id( &block )
-              repository( #{target }, #{type } ).each_with_id( &block )
+
+            define_method("each_#{name}_with_id") do |&block|
+              repository(target, type).each_with_id(&block)
             end
-_END_OF_EVAL_
           end
         end
 

data/test/data/nexml/test.xml

@@ -0,0 +1,69 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<nex:nexml
+    version="0.9"
+    generator="eclipse"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns:xml="http://www.w3.org/XML/1998/namespace"
+    xmlns:nex="http://www.nexml.org/2009"
+    xmlns="http://www.nexml.org/2009"
+    xsi:schemaLocation="http://www.nexml.org/2009 http://www.nexml.org/2009/nexml.xsd">
+
+    <otus id="taxa1" label="A taxa block">
+        <otu id="o1" label="A taxon"/>
+        <otu id="o2" label="A taxon"/>
+    </otus>
+    <trees otus="taxa1" id="trees1" label="A tree container">
+        <tree id="tree1" xsi:type="nex:FloatTree" label="A float tree">
+            <node id="n1" label="A node" root="true" otu="o1"/>
+            <node id="n2" label="A node"/>
+            <rootedge id="re1" label="A rootedge" target="n1" length="0.5"/>
+            <edge source="n1" target="n2" id="e1" length="0.4353" label="An edge"/>
+        </tree>
+        <network id="network1" xsi:type="nex:IntNetwork" label="An int network">
+            <node id="n1n1" label="A node" root="true" otu="o1"/>
+            <node id="n1n2" label="A node"/>
+            <edge source="n1n1" target="n1n2" id="n1e1" length="1" label="An edge"/>
+            <edge source="n1n2" target="n1n2" id="n1e2" length="0" label="An edge"/>
+        </network>
+    </trees>
+    <characters otus="taxa1" id="standardchars6" xsi:type="nex:StandardSeqs" label="Standard sequences">
+        <format>
+            <states id="sss1">
+                <state id="ss1" symbol="1"/>                                
+                <state id="ss2" symbol="2"/>                
+                <polymorphic_state_set symbol="4" id="ss4">                    
+                    <member state="ss1"/>
+                    <member state="ss2"/>                    
+                </polymorphic_state_set>
+                <uncertain_state_set symbol="5" id="ss5">
+                    <member state="ss2"/>                    
+                    <member state="ss1"/>
+                </uncertain_state_set>      
+            </states>
+            <char states="sss1" id="sc1"/>
+            <char states="sss1" id="sc2"/>
+        </format>    
+        <matrix>
+            <row id="sr1" otu="o1">
+                <seq>1 2</seq>
+            </row>
+            <row id="sr2" otu="o2">
+                <seq>2 2</seq>
+            </row>
+        </matrix>
+    </characters>
+    <characters otus="taxa1" id="m2" xsi:type="nex:StandardCells" label="Categorical characters">
+        <format>
+            <states id="sss2">
+                <state id="ss6" symbol="1"/>                                
+            </states>
+            <char states="sss2" id="sc3"/>
+        </format>
+
+        <matrix>
+            <row id="sr3" otu="o1">
+                <cell char="sc3" state="ss6"/>
+            </row>
+        </matrix>
+    </characters>
+</nex:nexml>

data/test/unit/bio/db/nexml/tc_factory.rb

@@ -0,0 +1,119 @@
+module Bio
+  module NeXML
+    class TestFactory < Test::Unit::TestCase
+      def setup
+        @nexml = Bio::NeXML::Nexml.new
+        @otus = @nexml.create_otus
+      end
+
+      def test_otus
+        assert @otus.kind_of? Bio::NeXML::Otus
+      end
+      
+      def test_otu
+        otu = @otus.create_otu
+        assert otu.kind_of? Bio::NeXML::Otu
+      end
+      
+      def test_trees
+        trees = @nexml.create_trees( :otus => @otus )
+        otu = @otus.create_otu
+        assert_equal @otus, trees.otus
+        assert trees.instance_of? Bio::NeXML::Trees
+        
+        floattree = trees.create_tree        
+        assert floattree.kind_of? Bio::NeXML::Tree
+        assert floattree.kind_of? Bio::Tree
+        assert floattree.kind_of? Bio::NeXML::FloatTree
+        floatnode = floattree.create_node( :otu => otu )
+        assert floatnode.kind_of? Bio::NeXML::Node
+        assert floatnode.kind_of? Bio::Tree::Node
+        assert_equal otu, floatnode.otu        
+        
+        floatedge = floattree.create_edge( :source => floatnode, :target => floatnode )
+        assert floatedge.kind_of? Bio::NeXML::Edge
+        assert floatedge.kind_of? Bio::Tree::Edge
+        assert floatedge.kind_of? Bio::NeXML::FloatEdge
+        floatrootedge = floattree.create_rootedge( :target => floatnode )
+        assert floatrootedge.kind_of? Bio::NeXML::Edge
+        assert floatrootedge.kind_of? Bio::Tree::Edge
+        assert floatrootedge.kind_of? Bio::NeXML::RootEdge
+        assert floatrootedge.kind_of? Bio::NeXML::FloatRootEdge
+        
+        inttree = trees.create_tree( true )
+        assert inttree.kind_of? Bio::NeXML::Tree
+        assert inttree.kind_of? Bio::Tree
+        assert inttree.kind_of? Bio::NeXML::IntTree
+        intedge = inttree.create_edge
+        assert intedge.kind_of? Bio::NeXML::Edge
+        assert intedge.kind_of? Bio::Tree::Edge
+        assert intedge.kind_of? Bio::NeXML::IntEdge
+        introotedge = inttree.create_rootedge
+        assert introotedge.kind_of? Bio::NeXML::Edge
+        assert introotedge.kind_of? Bio::Tree::Edge
+        assert introotedge.kind_of? Bio::NeXML::RootEdge
+        assert introotedge.kind_of? Bio::NeXML::IntRootEdge        
+        
+        floatnetwork = trees.create_network
+        assert floatnetwork.kind_of? Bio::NeXML::Tree
+        assert floatnetwork.kind_of? Bio::Tree
+        assert floatnetwork.kind_of? Bio::NeXML::FloatNetwork
+        floatnedge = floatnetwork.create_edge
+        assert floatnedge.kind_of? Bio::NeXML::Edge
+        assert floatnedge.kind_of? Bio::Tree::Edge
+        assert floatnedge.kind_of? Bio::NeXML::FloatEdge
+        
+        intnetwork = trees.create_network( true )
+        assert intnetwork.kind_of? Bio::NeXML::Tree
+        assert intnetwork.kind_of? Bio::Tree
+        assert intnetwork.kind_of? Bio::NeXML::IntNetwork
+        intnedge = intnetwork.create_edge
+        assert intnedge.kind_of? Bio::NeXML::Edge
+        assert intnedge.kind_of? Bio::Tree::Edge
+        assert intnedge.kind_of? Bio::NeXML::IntEdge        
+      end
+      def test_characters_seqs
+        otu = @otus.create_otu
+        dnaseqs = @nexml.create_characters( "Dna", false, :otus => @otus )
+        assert dnaseqs.kind_of? Bio::NeXML::Characters
+        assert dnaseqs.kind_of? Bio::NeXML::Dna
+        assert dnaseqs.kind_of? Bio::NeXML::DnaSeqs
+        assert_equal @otus, dnaseqs.otus
+        
+        format = dnaseqs.create_format
+        assert format.kind_of? Bio::NeXML::Format
+        assert_equal format, dnaseqs.format
+        
+        matrix = dnaseqs.create_matrix
+        assert matrix.kind_of? Bio::NeXML::Matrix
+        assert matrix.kind_of? Bio::NeXML::SeqMatrix
+        assert_equal matrix, dnaseqs.matrix
+        
+        row = matrix.create_row( :otu => otu )
+        assert row.kind_of? Bio::NeXML::Row
+        assert row.kind_of? Bio::NeXML::SeqRow
+        assert_equal otu, row.otu
+        
+        seq = 'ACATGCAG'
+        newrow = dnaseqs.create_raw( seq )
+        assert_equal newrow.sequences.first.value, seq
+      end
+      def test_characters_cells
+        otu1 = @otus.create_otu
+        otu2 = @otus.create_otu
+        standardcells = @nexml.create_characters( "Standard", true, :otus => @otus )
+        newrow1 = standardcells.create_raw('1 2 3 4 5')
+        newrow1.otu = otu1
+        newrow2 = standardcells.create_raw('1 2 3 4 5')
+        newrow2.otu = otu2
+        assert_equal otu1, newrow1.otu
+        assert_equal otu2, newrow2.otu
+        assert newrow1.kind_of? Bio::NeXML::Row
+        assert newrow1.kind_of? Bio::NeXML::CellRow
+        assert standardcells.kind_of? Bio::NeXML::Characters
+        assert standardcells.kind_of? Bio::NeXML::Standard
+        assert standardcells.kind_of? Bio::NeXML::StandardCells
+      end
+    end
+  end
+end

data/test/unit/bio/db/nexml/tc_mapper.rb

@@ -0,0 +1,78 @@
+module Bio
+  module NeXML
+    class TestMapper < Test::Unit::TestCase
+
+      class Target
+        include Bio::NeXML::Mapper
+
+        attr_accessor   :id
+        belongs_to      :source
+      end
+
+      class Source
+        include Bio::NeXML::Mapper
+
+        attr_accessor  :id
+        has_n          :targets
+      end
+
+      def setup
+        @s  = Source.new
+        @t1 = Target.new
+        @t1.id = 't1'
+        @t2 = Target.new
+        @t2.id = 't2'
+        @s.add_target( @t1 )
+      end
+
+      def test_has_target
+        t2 = Target.new
+        assert @s.has_target?( @t1 )
+        assert !@s.has_target?( t2 )
+      end
+
+      def test_get_target_by_id
+        assert_equal( @t1, @s.get_target_by_id( 't1' ) )
+        assert_nil( @s.get_target_by_id( 't2' ) )
+      end
+
+      def test_add_target
+        t2 = Target.new
+        t2.id = 't2'
+        @s.add_target( t2 )
+
+        assert @s.has_target?( t2 )
+        assert_equal( @s, t2.source )
+      end
+
+      def test_target
+        assert_equal( [ @t1 ], @s.targets )
+      end
+
+      def test_target=
+        t2 = Target.new
+        @s.targets = [ t2 ]
+        assert_equal( [ t2 ], @s.targets )
+        assert_equal( @s, t2.source )
+      end
+
+      def test_delete_target
+        assert_equal( @t1, @s.delete_target( @t1 ) )
+        assert_nil( @t1.source )
+      end
+
+      def test_source
+        assert_equal( @s, @t1.source )
+        assert( @s.has_target?( @t1 ) )
+      end
+
+      def test_source=
+        t2 = Target.new
+        t2.id = 't2'
+        t2.source = @s
+        assert_equal( @s, t2.source )
+        assert( @s.has_target?( t2 ) )
+      end
+    end #end TestOtu
+  end #end NeXML
+end #end Bio

data/test/unit/bio/db/nexml/tc_matrix.rb

@@ -0,0 +1,551 @@
+module Bio
+  module NeXML
+    class TestState < Test::Unit::TestCase
+      def setup
+        @state = Bio::NeXML::State.new( 'stateA', 'A' )
+      end
+
+      def test_new1
+        # if one argument given use it as id
+        s = Bio::NeXML::State.new( 'stateA' )
+        assert_equal 'stateA', s.id
+      end
+
+      def test_new2
+        # if two argument given use them as id and sybmol respectively
+        s = Bio::NeXML::State.new( 'stateA', 'A' )
+        assert_equal 'stateA', s.id
+        assert_equal 'A', s.symbol
+      end
+
+      def test_new3
+        # options hash as third argument
+        # preferred
+        s = Bio::NeXML::State.new( 'stateA', 'A', :label => 'A label' )
+        assert_equal 'stateA', s.id
+        assert_equal 'A', s.symbol
+        assert_equal 'A label', s.label
+      end
+
+      def test_new4
+        # options hash as second argument
+        s = Bio::NeXML::State.new( 'stateA', :symbol => 'A', :label => 'A label' )
+        assert_equal 'stateA', s.id
+        assert_equal 'A', s.symbol
+        assert_equal 'A label', s.label
+      end
+
+      def test_id
+        @state.id = 'state1'
+        assert_equal 'state1', @state.id
+      end
+
+      def test_symbol
+        @state.symbol = 1
+        assert_equal 1, @state.symbol
+      end
+
+      def test_label
+        @state.label = 'State'
+        assert_equal 'State', @state.label
+      end
+
+      def test_ambiguous
+        assert !@state.ambiguous?
+      end
+
+      def test_ambiguity
+        assert_nil @state.ambiguity
+      end
+
+      def test_to_str
+        assert_equal 'A', @state.to_str
+      end
+    end
+
+    class TestAmbiguousState < TestState
+      def setup
+        @members = [
+          %w|s1 A|,
+          %w|s2 B|,
+          %w|s3 C|,
+          %w|s4 D|,
+          %w|s5 E|
+        ].map { | pair | Bio::NeXML::State.new( *pair ) }
+
+        @state = Bio::NeXML::State.uncertain( 'state1', '?' )
+        @state.members = @members
+      end
+
+      def test_new5
+        s = Bio::NeXML::State.new( 'stateA', 'A', :ambiguity => :polymorphic )
+        assert s.ambiguous?
+        assert_equal :polymorphic, s.ambiguity
+      end
+
+      def test_new6
+        s = Bio::NeXML::State.new( 'stateA', 'A', :ambiguity => :uncertain, :members => @members )
+        assert_equal @members, s.members
+      end
+
+      def test_uncertain
+        s = Bio::NeXML::State.uncertain( 'stateA', 'A', :members => @members )
+        assert s.ambiguous?
+        assert_equal :uncertain, s.ambiguity
+        assert_equal @members, s.members
+      end
+
+      def test_polymorphic
+        s = Bio::NeXML::State.polymorphic( 'stateA', 'A', :members => @members )
+        assert s.ambiguous?
+        assert_equal :polymorphic, s.ambiguity
+        assert_equal @members, s.members
+      end
+
+      def test_ambiguous
+        assert @state.ambiguous?
+      end
+
+      def test_ambiguity
+        assert_equal :uncertain, @state.ambiguity
+      end
+
+      def test_add_member
+        s = Bio::NeXML::State.new( 's6', 'F' )
+        @state.add_member( s )
+        assert @state.has_member?( s )
+        assert_equal @state, s.state_set
+      end
+
+      def test_delete_member
+        s = @members[ 0 ]
+        assert_equal( s, @state.delete_member( s ) )
+        assert_nil s.state_set
+      end
+
+      def test_members
+        s = @members[ 0 ]
+        @state.members = [ s ]
+        assert_equal [ s ], @state.members
+        assert_equal @state, s.state_set
+      end
+
+      def test_include
+        assert @state.include?( @members[ 0 ] )
+      end
+      
+      def test_count
+        assert_equal @members.length, @state.count
+      end
+
+      def test_each
+      end
+
+      def test_each_with_symbol
+      end
+
+      def test_to_str
+        assert_equal '?', @state.to_str
+      end
+    end #end class TestAmbiguousState
+
+    class TestChar < Test::Unit::TestCase
+      def setup
+        @states = Bio::NeXML::States.new( 'states' )
+        @char = Bio::NeXML::Char.new( 'char1' )
+      end
+
+      def test_new1
+        # if one argument given use it as id
+        c = Bio::NeXML::Char.new( 'char1' )
+        assert_equal 'char1', c.id
+      end
+
+      def test_new2
+        # if two arguments given use the second as states
+        c = Bio::NeXML::Char.new( 'char1', @states )
+        assert_equal 'char1', c.id
+        assert_equal @states, c.states
+      end
+
+      def test_new3
+        # 3rd argument as optional hash
+        c = Bio::NeXML::Char.new( 'char1', @states, :label => 'A label' )
+        assert_equal 'char1', c.id
+        assert_equal @states, c.states
+        assert_equal 'A label', c.label
+      end
+
+      def test_new4
+        # 2nd argument as optional hash
+        c = Bio::NeXML::Char.new( 'char1', :states => @states, :label => 'A label' )
+        assert_equal 'char1', c.id
+        assert_equal @states, c.states
+        assert_equal 'A label', c.label
+      end
+
+      def test_id
+        @char.id = 'char2'
+        assert_equal 'char2', @char.id
+      end
+
+      def test_label
+        @char.label = 'A label'
+        assert_equal 'A label', @char.label
+      end
+
+      def test_states
+        @char.states = @states
+        assert_equal @states, @char.states
+        assert @states.has_char?( @char )
+      end
+
+      def test_cells
+        cell = Bio::NeXML::Cell.new( @char )
+        assert_equal [ cell ], @char.cells
+      end
+    end
+
+    class TestStates < Test::Unit::TestCase
+      def setup
+        @ss = [
+          %w|s1 A|,
+          %w|s2 B|,
+          %w|s3 C|,
+          %w|s4 D|,
+          %w|s5 E|
+        ].map { | pair | Bio::NeXML::State.new( *pair ) }
+        @states = Bio::NeXML::States.new( 'states', :states => @ss )
+      end
+
+      def test_new1
+        # one argument => id
+        states = Bio::NeXML::States.new( 'states' )
+        assert_equal 'states', states.id
+      end
+
+      def test_new2
+        # second argument => optional hash
+        states = Bio::NeXML::States.new( 'states', :label => 'state container' )
+        assert_equal 'states', states.id
+        assert_equal 'state container', states.label
+      end
+
+      def test_id
+        @states.id = 'states1'
+        assert_equal 'states1', @states.id
+      end
+
+      def test_label
+        @states.label = 'a label'
+        assert_equal 'a label', @states.label
+      end
+
+      def test_add_state
+        s = Bio::NeXML::State.new( 's6', 'F' )
+        @states.add_state( s )
+        assert @states.include?( s )
+        assert_equal @states, s.states
+      end
+
+      def test_delete_state
+        s = @ss[ 0 ]
+        assert_equal s, @states.delete_state( s )
+        assert_nil s.states
+      end
+
+      def test_states
+        s = @ss[ 0 ]
+        @states.states = [ s ]
+        assert_equal [ s ], @states.states
+        assert_equal @states, s.states
+      end
+
+      def test_get_state_by_id
+        s = @ss[ 0 ]
+        assert_equal s, @states.get_state_by_id( s.id )
+      end
+
+      def test_has_state
+        assert @states.has_state?( @ss[ 0 ] )
+      end
+
+      def test_chars
+        char = Bio::NeXML::Char.new( 'char', @states )
+        assert_equal @states, char.states
+        assert_equal [ char ], @states.chars
+      end
+    end
+
+    class TestCell_new < Test::Unit::TestCase
+      # test Bio::NeXML::Cell.new as a cell can be initialized in mulitple ways
+      # depending on type( bound/ unbound ) and need.
+
+      def test_new1
+        # unbound cell, no options
+        cell = Bio::NeXML::Cell.new( 'A' )
+        assert_equal 'A', cell.value
+      end
+
+      def test_new2
+        # unbound cell, with options
+        cell = Bio::NeXML::Cell.new( 'A', :label => 'label' )
+        assert_equal 'A', cell.value
+        assert_equal 'label', cell.label
+      end
+
+      def test_new3
+        # bound cell, no options
+        ch = Bio::NeXML::Char.new( 'ch' )
+        s = Bio::NeXML::State.new( 'ss' )
+        cell = Bio::NeXML::Cell.new( ch, s )
+        assert_equal ch, cell.char
+        assert_equal s, cell.state
+      end
+
+      def test_new4
+        # bound cell, with options
+        ch = Bio::NeXML::Char.new( 'ch' )
+        s = Bio::NeXML::State.new( 'ss' )
+        cell = Bio::NeXML::Cell.new( ch, s, :label => 'label' )
+        assert_equal ch, cell.char
+        assert_equal s, cell.state
+        assert_equal 'label', cell.label
+      end
+
+      def test_new5
+        # all keyword args
+        ch = Bio::NeXML::Char.new( 'ch' )
+        s = Bio::NeXML::State.new( 'ss' )
+        cell = Bio::NeXML::Cell.new( :char => ch, :state => s, :label => 'label' )
+        assert_equal ch, cell.char
+        assert_equal s, cell.state
+        assert_equal 'label', cell.label
+      end
+    end
+
+    class TestUnboundCell < Test::Unit::TestCase
+      def setup
+        @cell = Bio::NeXML::Cell.new( 'A', :label => 'label' )
+      end
+
+      def test_state
+        assert_nil @cell.state
+      end
+
+      def test_char
+        assert_nil @cell.char
+      end
+
+      def test_bound
+        assert !@cell.bound?
+      end
+
+      def test_value
+        @cell.value = 'B'
+        assert_equal 'B', @cell.value
+      end
+    end
+
+    class TestBoundCell < Test::Unit::TestCase
+      def setup
+        @stateA = Bio::NeXML::State.new( 'stateA', 'A' )
+        @char = Bio::NeXML::Char.new( 'char' )
+        @cell = Bio::NeXML::Cell.new( :char => @char, :state => @stateA )
+      end
+
+      def test_state
+        s = Bio::NeXML::State.new( 'stateB', 'B' )
+        @cell.state = s
+        assert_equal s, @cell.state
+      end
+
+      def test_char
+        c = Bio::NeXML::Char.new( 'ch' )
+        @cell.char = c
+        assert_equal c, @cell.char
+      end
+
+      def test_value
+        assert_equal @stateA.symbol, @cell.value
+        @cell.value = 'B'
+        assert_not_equal 'B', @cell.value # since it is a bound cell
+        @stateA.symbol = 'B'
+        assert_equal 'B', @cell.value # a bound cell reflects the value of its state
+      end
+    end
+
+    class TestRow < Test::Unit::TestCase
+      def setup
+        @row = Bio::NeXML::Row.new( 'seq' )
+      end
+
+      def test_id
+        @row.id = 'seq1'
+        assert_equal 'seq1', @row.id
+      end
+
+      def test_label
+        @row.label = 'a sequence'
+        assert_equal 'a sequence', @row.label
+      end
+
+      def test_otu
+        otu = Bio::NeXML::Otu.new( 'otu' )
+        @row.otu = otu
+        assert_equal otu, @row.otu
+        assert_equal [ @row ], otu.rows
+      end
+    end
+
+    class TestMatrix < Test::Unit::TestCase
+      def setup
+        @ss = [
+          %w|s1 A|,
+          %w|s2 B|,
+          %w|s3 C|,
+          %w|s4 D|,
+          %w|s5 E|
+        ].map { | pair | Bio::NeXML::State.new( *pair ) }
+        @states = Bio::NeXML::States.new( 'states', :states => @ss )
+
+        @char1 = Bio::NeXML::Char.new( 'char1', :states => @states )
+        @char2 = Bio::NeXML::Char.new( 'char2', :states => @states )
+
+        @sequence = Bio::NeXML::Sequence.new( :value => 'ABCDE' )
+        @row = Bio::NeXML::SeqRow.new( 'row1' )
+        @matrix = Bio::NeXML::Protein.new( 'matrix1' )
+        @format = Bio::NeXML::Format.new
+        @format.add_states( @states )
+        @format.chars = [ @char1, @char2 ]
+        @row.add_sequence( @sequence )
+      end
+
+      def test_id
+        @matrix.id = 'id'
+        assert_equal 'id', @matrix.id
+      end
+
+      def test_label
+        @matrix.label = 'label'
+        assert_equal 'label', @matrix.label
+      end
+
+      def test_nexml; end
+
+      def test_otus
+        otus = Bio::NeXML::Otus.new( 'otus' )
+        @matrix.otus = otus
+        assert_equal otus, @matrix.otus
+        assert_equal [ @matrix ], otus.characters
+      end
+
+      def test_add_states
+        ss = Bio::NeXML::States.new( 'ss' )
+        @format.add_states( ss )
+        assert @format.has_states?( ss )
+        assert_equal @format, ss.format
+      end
+
+      def test_add_char
+        ch = Bio::NeXML::Char.new( 'ch' )
+        @format.add_char( ch )
+        assert @format.has_char?( ch )
+        assert_equal @format, ch.format
+      end
+
+      def test_add_sequence
+        seq = Bio::NeXML::Sequence.new
+        @row.add_sequence( seq )
+        assert @row.has_sequence?( seq )
+        assert_equal @row, seq.seqrow
+      end
+
+      def test_delete_states
+        assert_equal @states, @format.delete_states( @states )
+        assert !@format.has_states?( @states )
+        assert_nil @states.format
+      end
+
+      def test_delete_char
+        assert_equal @char1, @format.delete_char( @char1 )
+        assert !@format.has_char?( @char1 )
+        assert_nil @char1.format
+      end
+
+      def test_delete_sequence
+        assert_equal @sequence, @row.delete_sequence( @sequence )
+        assert !@row.has_sequence?( @sequence )
+        assert_nil @sequence.row
+      end
+
+      def test_states
+        assert_equal [ @states ], @format.states
+        ss = Bio::NeXML::States.new( 'ss' )
+        @format.states = [ ss ]
+        assert_equal [ ss ], @format.states
+      end
+
+      def test_chars
+        assert_equal [ @char1, @char2 ], @format.chars
+        ch = Bio::NeXML::Char.new( 'ch' )
+        @format.chars = [ ch ]
+        assert_equal [ ch ], @format.chars
+      end
+
+      def test_sequences
+        assert_equal [ @sequence ], @row.sequences
+        seq = Bio::NeXML::Sequence.new
+        @row.sequences = [ seq ]
+        assert_equal [ seq ], @row.sequences
+      end
+
+      def test_get_states_by_id
+        assert_equal @states, @format.get_states_by_id( 'states' )
+      end
+
+      def test_get_char_by_id
+        assert_equal @char1, @format.get_char_by_id( 'char1' )
+      end
+
+      def test_each_states
+        c = 0
+        @format.each_states do |s|
+          assert @format.has_states?( s )
+          c += 1
+        end
+        assert_equal 1, c
+      end
+      
+      def test_each_char
+        c = 0
+        @format.each_char do |ch|
+          assert @format.has_char?( ch )
+          c += 1
+        end
+        assert_equal 2, c
+      end
+
+      def test_each_sequence
+        c = 0
+        @row.each_sequence do |s|
+          assert @row.has_sequence?( s )
+          c += 1
+        end
+        assert_equal 1, c
+      end
+
+      def test_number_of_states
+        assert_equal 1, @format.number_of_states
+      end
+
+      def test_number_of_chars
+        assert_equal 2, @format.number_of_chars
+      end
+
+      def test_number_of_sequences
+        assert_equal 1, @row.number_of_sequences
+      end
+    end
+  end #end module NeXML
+end #end module Bio