#
# = 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