bio 1.5.2 → 1.6.0.pre.20181210

data/lib/bio/db/phyloxml/phyloxml_elements.rb

@@ -1,1197 +0,0 @@
-#
-# = bio/db/phyloxml_elements.rb - PhyloXML Element classes
-#
-# Copyright::   Copyright (C) 2009
-#               Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
-# License::     The Ruby License
-#
-#
-# == Description
-#
-# This file containts the classes to represent PhyloXML elements.
-#
-# == References
-#
-# * http://www.phyloxml.org
-#
-# * https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby
-
-require 'bio/tree'
-require 'bio/sequence'
-require 'bio/reference'
-
-# Autoload definition
-module Bio
-  module PhyloXML
-    autoload :Parser, 'bio/db/phyloxml/phyloxml_parser'
-    autoload :Writer, 'bio/db/phyloxml/phyloxml_writer'
-  end
-end
-
-require 'libxml'
-
-module Bio
-
-   # This is general Taxonomy class.
-
-  class Taxonomy
-    #pattern = [a-zA-Z0-9_]{2,10} Can refer to any code/abbreviation/mnemonic, such as Bsu for Bacillus subtilis.
-    attr_accessor :code
-
-    # String.
-    attr_accessor :scientific_name
-    # An array of strings
-    attr_accessor :common_names
-
-    # value comes from list: domain kingdom, subkingdom, branch, infrakingdom,
-    # superphylum, phylum, subphylum, infraphylum, microphylum, superdivision,
-    # division, subdivision, infradivision, superclass, class, subclass,
-    # infraclass, superlegion, legion, sublegion, infralegion, supercohort,
-    # cohort, subcohort, infracohort, superorder, order, suborder,
-    # superfamily, family, subfamily, supertribe, tribe, subtribe, infratribe,
-    # genus, subgenus, superspecies, species, subspecies, variety, subvariety,
-    # form, subform, cultivar, unknown, other
-    attr_accessor :rank
-
-    # is used to keep the authority, such as 'J. G. Cooper, 1863', associated with the 'scientific_name'.
-    attr_accessor :authority
-
-    # An array of strings. Holds synonyms for scientific names or common names.
-    attr_accessor :synonyms
-
-
-    def initialize
-      @common_names = []
-      @synonyms = []
-    end
-  end
-
-module PhyloXML
-
-  
-  # Taxonomy class
-  class Taxonomy < Bio::Taxonomy
-    # String. Unique identifier of a taxon.
-    attr_accessor :taxonomy_id
-    #Used to link other elements to a taxonomy (on the xml-level)
-    attr_accessor :id_source
-    # Uri object
-    attr_accessor :uri
-
-    # Array of Other objects. Used to save additional information from other than
-    # PhyloXML namspace.
-    attr_accessor :other
-
-    def initialize
-      super
-      @other = []
-    end
-
-    # Converts elements to xml representation. Called by PhyloXML::Writer class.
-    def to_xml
-      taxonomy = LibXML::XML::Node.new('taxonomy')
-      taxonomy["type"] = @type if (defined? @type) && @type
-      taxonomy["id_source"] = @id_source if (defined? @id_source) && @id_source
-
-      PhyloXML::Writer.generate_xml(taxonomy, self, [[:complex, 'id', (defined? @taxonomy_id) ? @taxonomy_id : nil],
-        [:pattern, 'code', (defined? @code) ? @code : nil, Regexp.new("^[a-zA-Z0-9_]{2,10}$")],
-        [:simple, 'scientific_name', (defined? @scientific_name) ? @scientific_name : nil],
-        [:simple, 'authority', (defined? @authority) ? @authority : nil],
-        [:simplearr, 'common_name', (defined? @common_names) ? @common_names : nil],
-        [:simplearr, 'synonym', (defined? @synonyms) ? @synonyms : nil],
-        [:simple, 'rank', (defined? @rank) ? @rank : nil],
-        [:complex, 'uri',(defined? @uri) ? @uri : nil]])
-        #@todo anything else
-
-
-      return taxonomy
-    end
-
-  end
-
-  # Object to hold one phylogeny element (and its subelements.) Extended version of Bio::Tree.
-  class Tree < Bio::Tree
-    # String. Name of tree (name subelement of phylogeny element).
-    attr_accessor :name
-
-    # Id object.
-    attr_accessor :phylogeny_id
-
-    # String. Description of tree.
-    attr_accessor :description
-   
-    # Boolean. Can be used to indicate that the phylogeny is not allowed to be rooted differently (i.e. because it is associated with root dependent data, such as gene duplications).
-    attr_accessor :rerootable
-
-    # Boolean. Required element.
-    attr_accessor  :rooted
-
-    # Array of Property object. Allows for typed and referenced properties from external resources to be attached.
-    attr_accessor :properties
-
-    # CladeRelation object. This is used to express a typed relationship between two clades. For example it could be used to describe multiple parents of a clade.
-    attr_accessor :clade_relations
-
-    # SequenceRelation object. This is used to express a typed relationship between two sequences. For example it could be used to describe an orthology.
-    attr_accessor :sequence_relations
-
-    # Array of confidence object
-    attr_accessor :confidences
-
-    # String.
-    attr_accessor :branch_length_unit
-
-    # String. Indicate the type of phylogeny (i.e. 'gene tree').
-    attr_accessor :type
-
-    # String. Date
-    attr_accessor :date
-
-    # Array of Other objects. Used to save additional information from other than
-    # PhyloXML namspace.
-    attr_accessor :other
-
-   def initialize
-     super
-     @sequence_relations = []
-     @clade_relations = []
-     @confidences = []
-     @properties = []
-     @other = []
-   end
-
-  end
-
-
-  # == Description
-  # Class to hold clade element of phyloXML.
-  class Node
-
-    # Events at the root node of a clade (e.g. one gene duplication).
-    attr_accessor :events
-
-    # String. Used to link other elements to a clade (node) (on the xml-level).
-    attr_accessor :id_source
-
-    # String. Name of the node.
-    attr_accessor :name
-
-    # Float. Branch width for this node (including parent branch). Applies for the whole clade unless overwritten in sub-clades.
-    attr_reader :width
-
-    def width=(str)
-      @width = str.to_f
-    end
-
-    # Array of Taxonomy objects. Describes taxonomic information for a clade.
-    attr_accessor :taxonomies
-
-    # Array of Confidence objects. Indicates the support for a clade/parent branch.
-    attr_accessor :confidences
-
-    # BranchColor object. Apply for the whole clade unless overwritten in sub-clade.
-    attr_accessor :color
-
-    # Id object
-    attr_accessor :node_id
-
-    # Array of Sequence objects. Represents a molecular sequence (Protein, DNA, RNA) associated with a node.
-    attr_accessor :sequences
-
-    # BinaryCharacters object. The names and/or counts of binary characters present, gained, and lost at the root of a clade.
-    attr_accessor :binary_characters
-
-    # Array of Distribution objects. The geographic distribution of the items of a clade (species, sequences), intended for phylogeographic applications.
-    attr_accessor :distributions
-
-    # Date object. A date associated with a clade/node.
-    attr_accessor :date
-
-    #Array of Reference objects. A literature reference for a clade.
-    attr_accessor :references
-
-    #An array of Property objects, for example depth for sea animals.
-    attr_accessor :properties
-
-    # Array of Other objects. Used to save additional information from other than
-    # PhyloXML namspace.
-    attr_accessor :other
-
-    def initialize
-      @confidences = []
-      @sequences = []
-      @taxonomies = []
-      @distributions = []
-      @references = []
-      @properties = []
-      @other = []
-    end
-
-
-    # Converts to a Bio::Tree::Node object. If it contains several taxonomies 
-    # Bio::Tree::Node#scientific name will get the scientific name of the first 
-    # taxonomy.
-    # 
-    # If there are several confidence values, the first with bootstrap type will 
-    # be returned as Bio::Tree::Node#bootstrap
-    #
-    # tree = phyloxmlparser.next_tree
-    #
-    # node = tree.get_node_by_name("A").to_biotreenode
-    #
-    # ---
-    # *Returns*:: Bio::Tree::Node
-    def to_biotreenode
-      node = Bio::Tree::Node.new
-      node.name = @name
-      node.scientific_name = @taxonomies[0].scientific_name if not @taxonomies.empty?
-      #@todo what if there are more?
-      node.taxonomy_id = @taxonomies[0].taxononmy_id if @taxonomies[0] != nil
-
-      if not @confidences.empty?
-        @confidences.each do |confidence|
-          if confidence.type == "bootstrap"
-            node.bootstrap = confidence.value
-            break
-          end
-        end
-      end      
-      return node
-    end
-
-    # Extracts the relevant information from node (specifically taxonomy and
-    # sequence) to create Bio::Sequence object. Node can have several sequences,
-    # so parameter to this method is to specify which sequence to extract. 
-    #
-    # ---
-    # *Returns*:: Bio::Sequence
-    def extract_biosequence(seq_i=0)
-
-      seq = @sequences[seq_i].to_biosequence
-      seq.classification = []
-      @taxonomies.each do |t|
-        seq.classification << t.scientific_name
-        if t.rank == "species"
-          seq.species = t.scientific_name
-        end
-      end
-
-      #seq.division => .. http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_2
-      # It doesn't seem there is anything in PhyloXML corresponding to this.
-
-      return seq
-    end
-
-    # Converts elements to xml representation. Called by PhyloXML::Writer class.
-    def to_xml(branch_length,  write_branch_length_as_subelement)
-      clade = LibXML::XML::Node.new('clade')
-      
-      PhyloXML::Writer.generate_xml(clade, self, [[:simple, 'name', (defined? @name) ? @name : nil]])
-
-      if branch_length != nil       
-        if write_branch_length_as_subelement
-          clade << LibXML::XML::Node.new('branch_length', branch_length.to_s)
-        else
-          clade["branch_length"] = branch_length.to_s
-        end
-      end
-
-      #generate all elements, except clade
-      PhyloXML::Writer.generate_xml(clade, self, [
-          [:attr, "id_source"],
-          [:objarr, 'confidence', 'confidences'],
-          [:simple, 'width', (defined? @width) ? @width : nil],
-          [:complex, 'branch_color', (defined? @branch_color) ? @branch_color : nil],
-          [:simple, 'node_id', (defined? @node_id) ? @node_id : nil],
-          [:objarr, 'taxonomy', 'taxonomies'],
-          [:objarr, 'sequence', 'sequences'],
-          [:complex, 'events', (defined? @events) ? @events : nil],
-          [:complex, 'binary_characters', (defined? @binary_characters) ? @binary_characters : nil],
-          [:objarr, 'distribution', 'distributions'],
-          [:complex, 'date', (defined? @date) ? @date : nil],
-          [:objarr, 'reference', 'references'],
-          [:objarr, 'propery', 'properties']])
-     
-      return clade
-    end
-
-  end #Node
-
-  # == Description
-  # Events at the root node of a clade (e.g. one gene duplication).
-  class Events
-    #value comes from list: transfer, fusion, speciation_or_duplication, other, mixed, unassigned
-    attr_reader :type
-
-    # Integer
-    attr_reader :duplications, :speciations, :losses
-
-    # Confidence object
-    attr_reader :confidence
-
-    #---
-    #def confidence=(type, value)
-    #  @confidence = Confidence.new(type, value)
-    #end
-    #+++
-
-    # Confidence object
-    def confidence=(conf)
-      @confidence = conf
-    end
-
-    # Integer
-    def duplications=(str)
-      @duplications = str.to_i
-    end
-
-    # Integer
-    def losses=(str)
-      @losses = str.to_i
-    end
-
-    # Integer
-    def speciations=(str)
-      @speciations=str.to_i
-    end
-
-    #value comes from list: transfer, fusion, speciation_or_duplication, other, mixed, unassigned
-    def type=(str)
-      @type = str
-      #@todo add unit test for this
-      if not ['transfer','fusion','speciation_or_duplication','other','mixed', 'unassigned'].include?(str)
-        raise "Warning #{str} is not one of the allowed values"
-      end
-    end
-
-    # Converts elements to xml representation. Called by PhyloXML::Writer class.
-    def to_xml
-      #@todo add unit test
-      events = LibXML::XML::Node.new('events')
-      PhyloXML::Writer.generate_xml(events, self, [
-        [:simple, 'type', (defined? @type) ? @type : nil],
-        [:simple, 'duplications', (defined? @duplications) ? @duplications : nil],
-        [:simple, 'speciations', (defined? @speciations) ? @speciations : nil],
-        [:simple, 'losses', (defined? @losses) ? @losses : nil],
-        [:complex, 'confidence', (defined? @confidence) ? @confidence : nil]])
-      return events
-    end
-
-  end
-
-    # A general purpose confidence element. For example this can be used to express
-    # the bootstrap support value of a clade (in which case the 'type' attribute
-    # is 'bootstrap').
-    class Confidence
-      # String. The type of confidence measure, for example, bootstrap.
-      attr_accessor :type
-      # Float. The value of confidence measure.
-      attr_accessor :value
-
-      def initialize(type, value)
-        @type = type
-        @value = value.to_f
-      end
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        if @type == nil
-          raise "Type is a required attribute for confidence."
-        else
-          confidence = LibXML::XML::Node.new('confidence', @value.to_s)
-          confidence["type"] = @type          
-          return confidence
-        end
-      end
-    end
-
-    # == Description
-    #
-    # The geographic distribution of the items of a clade (species, sequences),
-    # intended for phylogeographic applications. 
-    class Distribution
-      # String. Free text description of location.
-      attr_accessor :desc
-      # Array of Point objects. Holds coordinates of the location.
-      attr_accessor :points
-      # Array of Polygon objects.
-      attr_accessor :polygons
-
-      def initialize
-        @points = []
-        @polygons = []
-      end
-
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        distr = LibXML::XML::Node.new('distribution')
-        PhyloXML::Writer.generate_xml(distr, self, [
-            [:simple, 'desc', @desc],
-            [:objarr, 'point', 'points'],
-            [:objarr, 'polygon', 'polygons']])
-        return distr
-      end
-      
-    end #Distribution class
-
-
-    # == Description
-    #
-    # The coordinates of a point with an optional altitude. Required attribute
-    # 'geodetic_datum' is used to indicate the geodetic datum (also called
-    # 'map datum'), for example Google's KML uses 'WGS84'.
-    class Point
-      # Float. Latitude
-      attr_reader :lat
-
-      # Float. Longitute
-      attr_reader :long
-      
-      # Float. Altitude
-      attr_reader :alt
-
-      # String. Altitude unit.
-      attr_accessor :alt_unit
-
-      # Geodedic datum / map datum
-      attr_accessor :geodetic_datum
-
-      # Float. Latitude
-      def lat=(str)
-        @lat = str.to_f unless str.nil?
-      end
-
-      # Float. Longitute
-      def long=(str)
-        @long = str.to_f unless str.nil?
-      end
-
-      # Float. Altitude
-      def alt=(str)
-        @alt = str.to_f unless str.nil?
-      end
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        raise "Geodedic datum is a required attribute of Point element." if @geodetic_datum.nil?
-
-        p = LibXML::XML::Node.new('point')
-        p["geodetic_datum"] = @geodetic_datum
-        p["alt_unit"] = @alt_unit if @alt_unit != nil
-        PhyloXML::Writer.generate_xml(p, self, [
-            [:simple, 'lat', @lat],
-            [:simple, 'long', @long],
-            [:simple, 'alt', @alt]])
-        return p
-        #@todo check if characters are correctly generated, like Zuric
-      end
-
-    end
-
-
-    # == Description
-    #
-    # A polygon defined by a list of Points objects.
-    class Polygon
-      # Array of Point objects.
-      attr_accessor :points
-
-      def initialize
-        @points = []
-      end
-
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        if @points.length > 2          
-          pol = LibXML::XML::Node.new('polygon')
-          @points.each do |p|
-            pol << p.to_xml
-          end
-          return pol
-        end
-      end
-
-
-    end
-
-    # == Description
-    # Element Sequence is used to represent a molecular sequence (Protein, DNA,
-    # RNA) associated with a node.
-    class Sequence
-      # Type of sequence (rna, dna, protein)
-      attr_accessor :type
-
-      # Full name (e.g. muscle Actin )
-      attr_accessor :name
-
-      # String. Used to link with other elements.
-      attr_accessor :id_source
-
-      # String. One intended use for 'id_ref' is to link a sequence to a taxonomy
-      # (via the taxonomy's 'id_source') in the case of multiple sequences and taxonomies per node.
-      attr_accessor :id_ref
-
-      # short (maximal ten characters) symbol of the sequence (e.g. 'ACTM')
-      attr_accessor :symbol
-      # Accession object. Holds source and identifier for the sequence.
-      attr_accessor :accession
-      # String. Location of a sequence on a genome/chromosome
-      attr_accessor :location
-      # String. The actual sequence is stored here.
-      attr_reader :mol_seq
-
-      # Boolean. used to indicated that this molecular sequence is aligned with
-      # all other sequences in the same phylogeny for which 'is aligned' is true
-      # as well (which, in most cases, means that gaps were introduced, and that
-      # all sequences for which 'is aligned' is true must have the same length)
-      attr_reader :is_aligned
-      
-      # Uri object
-      attr_accessor :uri
-      # Array of Annotation objects. Annotations of molecular sequence.
-      attr_accessor :annotations
-      # DomainArchitecture object. Describes domain architecture of a protein.
-      attr_accessor :domain_architecture
-
-      # Array of Other objects. Used to save additional information from other than
-      # PhyloXML namspace.
-      attr_accessor :other
-
-      def initialize
-        @annotations = []
-        @other = []
-      end
-
-      def is_aligned=(str)
-        if str=='true'
-          @is_aligned=true
-        elsif str=='false'
-          @is_aligned = false
-        else
-          @is_aligned = nil
-        end
-      end
-
-      def is_aligned?
-        @is_aligned
-      end
-
-      def mol_seq=(str)
-        if str =~ /^[a-zA-Z\.\-\?\*_]+$/
-          @mol_seq = str
-        else
-          raise "mol_seq element of Sequence does not follow the pattern."
-        end
-      end
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        
-        seq = LibXML::XML::Node.new('sequence')
-        if (defined? @type) && @type
-          if ["dna", "rna", "protein"].include?(@type)
-            seq["type"] = @type
-          else 
-            raise "Type attribute of Sequence has to be one of dna, rna or a."
-          end
-        end
-        
-        PhyloXML::Writer.generate_xml(seq, self, [
-            [:attr, 'id_source'],
-            [:attr, 'id_ref'],
-            [:pattern, 'symbol', (defined? @symbol) ? @symbol : nil, Regexp.new("^\\S{1,10}$")],
-            [:complex, 'accession', (defined? @accession) ? @accession : nil],
-            [:simple, 'name', (defined? @name) ? @name : nil],
-            [:simple, 'location', (defined? @location) ? @location : nil]])
-
-        if (defined? @mol_seq) && @mol_seq
-          molseq = LibXML::XML::Node.new('mol_seq', @mol_seq)
-          molseq["is_aligned"] = @is_aligned.to_s if (defined? @is_aligned) && @is_aligned != nil
-          seq << molseq
-        end
-
-        PhyloXML::Writer.generate_xml(seq, self, [
-            #[:pattern, 'mol_seq', @mol_seq, Regexp.new("^[a-zA-Z\.\-\?\*_]+$")],
-            [:complex, 'uri', (defined? @uri) ? @uri : nil],
-            [:objarr, 'annotation', 'annotations'],
-            [:complex, 'domain_architecture', (defined? @domain_architecture) ? @domain_architecture : nil]])
-            #@todo test domain_architecture
-        #any
-        return seq
-      end
-
-      # converts Bio::PhyloXML:Sequence to Bio::Sequence object.
-      # ---
-      # *Returns*:: Bio::Sequence
-      def to_biosequence
-        #type is not a required attribute in phyloxml (nor any other Sequence
-        #element) it might not hold any value, so we will not check what type it is.
-        seq = Bio::Sequence.auto(@mol_seq)
-
-        seq.id_namespace = @accession.source
-        seq.entry_id = @accession.value
-        # seq.primary_accession = @accession.value could be this
-        seq.definition = @name
-        #seq.comments = @name //this one?
-        if (defined? @uri) && @uri
-          h = {'url' => @uri.uri,
-            'title' => @uri.desc }
-          ref = Bio::Reference.new(h)
-          seq.references << ref
-        end
-        seq.molecule_type = 'RNA' if @type == 'rna'
-        seq.molecule_type = 'DNA' if @type == 'dna'
-
-        #@todo deal with the properties. There might be properties which look
-        #like bio sequence attributes or features
-        return seq
-      end
-
-    end
-
-    # == Description
-    # Element Accession is used to capture the local part in a sequence
-    # identifier.
-    class Accession
-      #String. Source of the accession id. Example: "UniProtKB"
-      attr_accessor :source
-
-      #String. Value of the accession id. Example: "P17304"
-      attr_accessor :value
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        raise "Source attribute is required for Accession object." if @source == nil
-        accession = LibXML::XML::Node.new('accession', @value)
-        accession['source'] = @source
-        return accession
-      end
-
-    end
-
-    # A uniform resource identifier. In general, this is expected to be an URL
-    # (for example, to link to an image on a website, in which case the 'type'
-    # attribute might be 'image' and 'desc' might be  'image of a California
-    # sea hare')
-    class Uri
-      # String. Description of the uri. For example, image of a California sea hare'
-      attr_accessor :desc
-      # String. For example, image.
-      attr_accessor :type
-      # String. URL of the resource.
-      attr_accessor :uri 
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml        
-        if @uri != nil
-          xml_node = LibXML::XML::Node.new('uri', @uri)
-          Writer.generate_xml(xml_node, self, [
-            [:attr, 'desc'],
-            [:attr, 'type']])
-          return xml_node
-        end
-      end
-    end
-
-    # == Description
-    #
-    # The annotation of a molecular sequence. It is recommended to annotate by
-    # using the optional 'ref' attribute (some examples of acceptable values
-    # for the ref attribute: 'GO:0008270', 'KEGG:Tetrachloroethene degradation',
-    #  'EC:1.1.1.1').
-    class Annotation
-      # String. For example, 'GO:0008270', 'KEGG:Tetrachloroethene degradation',
-      # 'EC:1.1.1.1'
-      attr_accessor :ref
-      # String
-      attr_accessor :source
-      # String. evidence for a annotation as free text (e.g. 'experimental')
-      attr_accessor :evidence
-      # String. Type of the annotation.
-      attr_accessor :type
-      # String. Free text description. 
-      attr_accessor :desc
-      # Confidence object. Type and value of support for a annotation.
-      attr_accessor :confidence
-      # Array of Property objects. Allows for further, typed and referenced
-      # annotations from external resources
-      attr_accessor :properties
-      # Uri object.
-      attr_accessor :uri
-
-      def initialize
-        #@todo add unit test for this, since didn't break anything when changed from property to properties
-        @properties = []
-      end
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class. 
-      def to_xml
-        annot = LibXML::XML::Node.new('annotation')
-        annot["ref"] = @ref if (defined? @ref) && @ref
-        PhyloXML::Writer.generate_xml(annot, self, [[:simple, 'desc', (defined? @desc) ? @desc : nil],
-          [:complex, 'confidence', (defined? @confidence) ? @confidence : nil],
-          [:objarr, 'property', 'properties'],
-          [:complex, 'uri', (defined? @uri) ? @uri : nil]])
-        return annot
-      end
-    end
-
-    class Id
-      # The provider of Id, for example, NCBI.
-      attr_accessor :provider
-      # The value of Id. 
-      attr_accessor :value
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        xml_node = LibXML::XML::Node.new('id', @value)
-        xml_node["provider"] = @provider if @provider != nil
-        return xml_node
-      end
-    end
-
-    # == Description
-    # This indicates the color of a node when rendered (the color applies
-    # to the whole node and its children unless overwritten by the
-    # color(s) of sub clades).
-    class BranchColor
-      #Integer
-      attr_reader :red, :green, :blue
-
-      def red=(str)
-        @red = str.to_i
-      end
-
-      def green=(str)
-        @green = str.to_i
-      end
-
-      def blue=(str)
-        @blue = str.to_i
-      end
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        #@todo add unit test
-        if @red == nil
-          raise "Subelement red of BranchColor element should not be nil"
-        elsif @green == nil
-          raise "Subelement green of BranchColor element should not be nil"
-        elsif @blue == nil
-          raise "Subelement blue of BranchColor element should not be nil"
-        end
-
-        c = LibXML::XML::Node.new('branch_color')
-        PhyloXML::Writer.generate_xml(c, self, [
-            [:simple, 'red', @red],
-            [:simple, 'green', @green],
-            [:simple, 'blue', @blue]])
-        return c
-      end
-
-    end
-
-    # == Description
-    # A date associated with a clade/node. Its value can be numerical by
-    # using the 'value' element and/or free text with the 'desc' element'
-    # (e.g. 'Silurian'). If a numerical value is used, it is recommended to
-    # employ the 'unit' attribute to indicate the type of the numerical
-    # value (e.g. 'mya' for 'million years ago').
-    class Date
-      # String. Units in which value is stored.
-      attr_accessor :unit
-
-      # Free text description of the date.
-      attr_accessor :desc
-
-      # Integer. Minimum and maximum of the value.
-      attr_reader :minimum, :maximum
-
-      # Integer. Value of the date.
-      attr_reader :value
-
-      def minimum=(str)
-        @minimum = str.to_i
-      end
-
-      def maximum=(str)
-        @maximum = str.to_i
-      end
-
-      def value= (str)
-        @value = str.to_i
-      end
-
-      # Returns value + unit, for exampe "7 mya"
-      def to_s
-        return "#{value} #{unit}"
-      end
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        date = LibXML::XML::Node.new('date')
-        PhyloXML::Writer.generate_xml(date, self, [
-            [:attr, 'unit'],
-            [:simple, 'desc', (defined? @desc) ? @desc : nil],
-            [:simple, 'value', (defined? @value) ? @value : nil],
-            [:simple, 'minimum', (defined? @minimum) ? @minimum : nil],
-            [:simple, 'maximum', (defined? @maximum) ? @maximum : nil]])
-        return date
-      end
-
-    end
-
-    # == Description
-    # This is used describe the domain architecture of a protein. Attribute
-    # 'length' is the total length of the protein
-    class DomainArchitecture
-      # Integer. Total length of the protein
-      attr_reader :length
-
-      # Array of ProteinDomain objects.
-      attr_reader :domains
-
-      # Integer. Total length of the protein
-      def length=(str)
-        @length = str.to_i
-      end
-
-      def initialize
-        @domains = []
-      end
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        xml_node = LibXML::XML::Node.new('domain_architecture')
-        PhyloXML::Writer.generate_xml(xml_node, self,[
-              [:attr, 'length'],
-              [:objarr, 'domain', 'domains']])
-        return xml_node
-      end
-    end
-
-
-    # == Description
-    # To represent an individual domain in a domain architecture. The
-    # name/unique identifier is described via the 'id' attribute.
-    class ProteinDomain
-      #Float, for example to store E-values    4.7E-14
-      attr_reader :confidence
-      
-      # String
-      attr_accessor :id, :value
-
-      # Integer. Beginning of the domain.
-      attr_reader :from
-
-      # Integer. End of the domain.
-      attr_reader :to
-
-      # Integer. Beginning of the domain.
-      def from=(str)
-        @from = str.to_i
-      end
-
-      # Integer. End of the domain.
-      def to=(str)
-        @to = str.to_i
-      end
-      
-      #Float, for example to store E-values    4.7E-14
-      def confidence=(str)
-        @confidence = str.to_f
-      end
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        if @from == nil
-          raise "from attribute of ProteinDomain class is required."
-        elsif @to == nil
-          raise "to attribute of ProteinDomain class is required."
-        else
-          xml_node = LibXML::XML::Node.new('domain', @value)
-          xml_node["from"] = @from.to_s
-          xml_node["to"] = @to.to_s
-          xml_node["id"] = @id if (defined? @id) && @id
-          xml_node["confidence"] = @confidence.to_s
-
-          return xml_node
-        end
-
-      end
-
-    end
-
-
-    #Property allows for typed and referenced properties from external resources
-    #to be attached to 'Phylogeny', 'Clade', and 'Annotation'. The value of a
-    #property is its mixed (free text) content. Attribute 'datatype' indicates
-    #the type of a property and is limited to xsd-datatypes (e.g. 'xsd:string',
-    #'xsd:boolean', 'xsd:integer', 'xsd:decimal', 'xsd:float', 'xsd:double',
-    #'xsd:date', 'xsd:anyURI'). Attribute 'applies_to' indicates the item to
-    #which a property applies to (e.g. 'node' for the parent node of a clade,
-    #'parent_branch' for the parent branch of a clade). Attribute 'id_ref' allows
-    #to attached a property specifically to one element (on the xml-level).
-    #Optional attribute 'unit' is used to indicate the unit of the property.
-    #An example: <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 200 </property>
-    class Property
-      # String
-      attr_accessor :ref, :unit, :id_ref, :value
-
-      # String
-      attr_reader :datatype, :applies_to
-
-      def datatype=(str)
-         #@todo add unit test or maybe remove, if assume that xml is valid.
-        unless ['xsd:string','xsd:boolean','xsd:decimal','xsd:float','xsd:double',
-            'xsd:duration','xsd:dateTime','xsd:time','xsd:date','xsd:gYearMonth',
-            'xsd:gYear','xsd:gMonthDay','xsd:gDay','xsd:gMonth','xsd:hexBinary',
-            'xsd:base64Binary','xsd:anyURI','xsd:normalizedString','xsd:token',
-            'xsd:integer','xsd:nonPositiveInteger','xsd:negativeInteger',
-            'xsd:long','xsd:int','xsd:short','xsd:byte','xsd:nonNegativeInteger',
-            'xsd:unsignedLong','xsd:unsignedInt','xsd:unsignedShort',
-            'xsd:unsignedByte','xsd:positiveInteger'].include?(str)
-          raise "Warning: #{str} is not in the list of allowed values."
-        end
-        @datatype = str
-      end
-
-      def applies_to=(str)
-        unless ['phylogeny','clade','node','annotation','parent_branch','other'].include?(str)
-          puts "Warning: #{str} is not in the list of allowed values."
-        end
-        @applies_to = str
-      end
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        #@todo  write unit test for this
-        raise "ref is an required element of property"  if @ref.nil?
-        raise "datatype is an required element of property" if @datatype.nil?
-        raise "applies_to is an required element of property" if @applies_to.nil?
-
-        property = LibXML::XML::Node.new('property')
-        Writer.generate_xml(property, self, [
-            [:attr, 'ref'],
-            [:attr, 'unit'],
-            [:attr, 'datatype'],
-            [:attr, 'applies_to'],
-            [:attr, 'id_ref']])
-
-        property << @value if @value != nil
-        return property
-      end
-    end
-
-    # == Description
-    # A literature reference for a clade. It is recommended to use the 'doi'
-    # attribute instead of the free text 'desc' element whenever possible.
-    class Reference
-      # String. Digital Object Identifier.
-      attr_accessor :doi
-
-      # String. Free text description.
-      attr_accessor :desc
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        ref = LibXML::XML::Node.new('reference')
-        Writer.generate_xml(ref, self, [
-              [:attr, 'doi'],
-              [:simple, 'desc', (defined? @desc) ? @desc : nil]])
-         return ref
-      end
-
-    end
-
-    # == Description
-    #
-    # This is used to express a typed relationship between two clades.
-    # For example it could be used to describe multiple parents of a clade.
-    class CladeRelation
-      # Float
-      attr_reader :distance
-      # String. Id of the referenced parents of a clade.
-      attr_accessor :id_ref_0, :id_ref_1
-      # String
-      attr_accessor :type
-      # Confidence object
-      attr_accessor :confidence
-
-      # Float
-      def distance=(str)
-        @distance = str.to_f
-      end
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        if @id_ref_0 == nil or @id_ref_1 == nil or @type == nil
-          raise "Attributes id_ref_0, id_ref_1, type are required elements by SequenceRelation element."
-        else
-          cr = LibXML::XML::Node.new('clade_relation')
-          Writer.generate_xml(cr, self, [
-              [:attr, 'id_ref_0'],
-              [:attr, 'id_ref_1'],
-              [:attr, 'distance'],
-              [:attr, 'type'],
-              [:complex, 'confidence', (defined? @confidnece) ? @confidnece : nil]])
-
-          return cr
-        end
-      end
-
-    end
-
-
-    # == Description
-    # The names and/or counts of binary characters present, gained, and
-    # lost at the root of a clade.
-    class BinaryCharacters
-      attr_accessor :bc_type, :gained, :lost, :present, :absent
-      attr_reader :gained_count, :lost_count, :present_count, :absent_count
-
-      def gained_count=(str)
-        @gained_count = str.to_i
-      end
-
-      def lost_count=(str)
-        @lost_count = str.to_i
-      end
-
-      def present_count=(str)
-        @present_count = str.to_i
-      end
-
-      def absent_count=(str)
-        @absent_count = str.to_i
-      end
-
-      def initialize
-        @gained = []
-        @lost = []
-        @present = []
-        @absent = []
-      end
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        bc = LibXML::XML::Node.new('binary_characters')
-        bc['type'] = @bc_type
-        PhyloXML::Writer.generate_xml(bc, self, [
-            [:attr, 'gained_count'],
-            [:attr, 'lost_count'],
-            [:attr, 'present_count'],
-            [:attr, 'absent_count']])
-
-        if not @gained.empty?
-          gained_xml = LibXML::XML::Node.new('gained')
-          PhyloXML::Writer.generate_xml(gained_xml, self, [[:simplearr, 'bc', @gained]])
-          bc << gained_xml
-        end
-
-        if not @lost.empty?
-          lost_xml = LibXML::XML::Node.new('lost')
-          PhyloXML::Writer.generate_xml(lost_xml, self, [[:simplearr, 'bc', @lost]])
-          bc << lost_xml
-        end
-
-        if not @present.empty?
-          present_xml = LibXML::XML::Node.new('present')
-          PhyloXML::Writer.generate_xml(present_xml, self, [[:simplearr, 'bc', @present]])
-          bc << present_xml
-        end
-
-        if not @absent.empty?
-          absent_xml = LibXML::XML::Node.new('absent')
-          PhyloXML::Writer.generate_xml(absent_xml, self, [[:simplearr, 'bc', @absent]])
-          bc << absent_xml
-        end
-
-        return bc
-      end
-
-
-    end
-
-    # == Description
-    # This is used to express a typed relationship between two sequences.
-    # For example it could be used to describe an orthology (in which case
-    # attribute 'type' is 'orthology').
-    class SequenceRelation
-      # String
-      attr_accessor :id_ref_0, :id_ref_1
-
-      # String. Allowed values: "orthology", "one_to_one_orthology",
-      # "super_orthology", "paralogy", "ultra_paralogy", "xenology",
-      # "unknown", "other"
-      attr_reader :type
-
-      # Float
-      attr_reader :distance
-
-      #@todo it has Confidences objects.
-
-      def distance=(str)
-        @distance = str.to_f if str != nil
-      end
-
-      # String. Allowed values: "orthology", "one_to_one_orthology",
-      # "super_orthology", "paralogy", "ultra_paralogy", "xenology",
-      # "unknown", "other"
-      def type=(str)
-        #@todo do warning instead?
-        #@todo do validation at actually writing xml
-        allowed_values = ["orthology", "one_to_one_orthology", "super_orthology", "paralogy",
-            "ultra_paralogy", "xenology", "unknown", "other"]
-        if not allowed_values.include? str
-          raise "SequenceRelation#type has to be one one of #{allowed_values.join("; ")}"
-        else
-          @type = str
-        end
-      end
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        if @id_ref_0 == nil or @id_ref_1 == nil or @type == nil
-          raise "Attributes id_ref_0, id_ref_1, type are required elements by SequenceRelation element."
-        else
-          sr = LibXML::XML::Node.new('sequence_relation')
-          sr['id_ref_0'] = @id_ref_0
-          sr['id_ref_1'] = @id_ref_1
-          sr['distance'] = @distance.to_s if (defined? @distance) && @distance
-          sr['type'] = @type
-          return sr
-        end
-      end
-
-    end
-
-    class Other
-      attr_accessor :element_name, :attributes, :children, :value
-      
-      def initialize
-        @children = []
-        @attributes = Hash.new
-      end
-
-      # Converts elements to xml representation. Called by PhyloXML::Writer class.
-      def to_xml
-        o = LibXML::XML::Node.new(@element_name)
-        @attributes.each do |key, value|
-          o[key] = value
-        end
-        o << value if value != nil
-        children.each do |child_node|
-          o << child_node.to_xml
-        end
-        return o
-      end
-      
-    end
-
-
-end #module PhyloXML
-
-end #end module Bio