bio 1.5.1 → 2.0.2

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

@@ -1,1001 +0,0 @@
-#
-# = bio/db/phyloxml_parser.rb - PhyloXML parser
-#
-# Copyright::   Copyright (C) 2009
-#               Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
-# License::     The Ruby License
-#
-#
-# == Description
-#
-# This file containts parser for PhyloXML.
-#
-# == Requirements
-# 
-# Libxml2 XML parser is required. Install libxml-ruby bindings from
-# http://libxml.rubyforge.org or
-#
-#   gem install -r libxml-ruby
-#
-# == References
-#
-# * http://www.phyloxml.org
-#
-# * https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby
-
-
-require 'uri'
-require 'libxml'
-
-require 'bio/tree'
-require 'bio/db/phyloxml/phyloxml_elements'
-
-
-module Bio
-
-module PhyloXML
-
-
-
-
-  # == Description
-  #
-  # Bio::PhyloXML::Parser is for parsing phyloXML format files.
-  # 
-  # == Requirements
-  #
-  # Libxml2 XML parser is required. Install libxml-ruby bindings from
-  # http://libxml.rubyforge.org or
-  #
-  #   gem install -r libxml-ruby
-  #
-  # == Usage
-  #
-  #   require 'bio'
-  #
-  #  # Create new phyloxml parser
-  #  phyloxml = Bio::PhyloXML::Parser.open('example.xml')
-  #
-  #  # Print the names of all trees in the file
-  #  phyloxml.each do |tree|
-  #    puts tree.name
-  #  end
-  #
-  #
-  # == References
-  #
-  # http://www.phyloxml.org/documentation/version_100/phyloxml.xsd.html
-  #
-  class Parser
-
-    include LibXML
-
-    # After parsing all the trees, if there is anything else in other xml format,
-    # it is saved in this array of PhyloXML::Other objects
-    attr_reader :other
-
-    # Initializes LibXML::Reader and reads the file until it reaches the first
-    # phylogeny element.
-    #
-    # Example: Create a new Bio::PhyloXML::Parser object.
-    #
-    #   p = Bio::PhyloXML::Parser.open("./phyloxml_examples.xml")
-    #
-    # If the optional code block is given, Bio::PhyloXML object is passed to
-    # the block as an argument. When the block terminates, the Bio::PhyloXML
-    # object is automatically closed, and the open method returns the value
-    # of the block.
-    #
-    # Example: Get the first tree in the file.
-    #
-    #   tree = Bio::PhyloXML::Parser.open("example.xml") do |px|
-    #     px.next_tree
-    #   end
-    #
-    # ---
-    # *Arguments*:
-    # * (required) _filename_: Path to the file to parse.
-    # * (optional) _validate_: Whether to validate the file against schema or not. Default value is true.
-    # *Returns*:: (without block) Bio::PhyloXML::Parser object
-    # *Returns*:: (with block) the value of the block
-    def self.open(filename, validate=true)
-      obj = new(nil, validate)
-      obj.instance_eval {
-        filename = _secure_filename(filename)
-        _validate(:file, filename) if validate
-        # XML::Parser::Options::NONET for security reason
-        @reader = XML::Reader.file(filename,
-                                   { :options =>
-                                     LibXML::XML::Parser::Options::NONET })
-        _skip_leader
-      }
-      if block_given? then
-        begin
-          ret = yield obj
-        ensure
-          obj.close if obj and !obj.closed?
-        end
-        ret
-      else
-        obj
-      end
-    end
-
-    # Initializes LibXML::Reader and reads the file until it reaches the first
-    # phylogeny element.
-    #
-    # Create a new Bio::PhyloXML::Parser object.
-    #
-    #   p = Bio::PhyloXML::Parser.open_uri("http://www.phyloxml.org/examples/apaf.xml")
-    #
-    # If the optional code block is given, Bio::PhyloXML object is passed to
-    # the block as an argument. When the block terminates, the Bio::PhyloXML
-    # object is automatically closed, and the open_uri method returns the
-    # value of the block.
-    #
-    # ---
-    # *Arguments*:
-    # * (required) _uri_: (URI or String) URI to the data to parse
-    # * (optional) _validate_: For URI reader, the "validate" option is ignored and no validation is executed.
-    # *Returns*:: (without block) Bio::PhyloXML::Parser object
-    # *Returns*:: (with block) the value of the block
-    def self.open_uri(uri, validate=true)
-      case uri
-      when URI
-        uri = uri.to_s
-      else
-        # raises error if not a String
-        uri = uri.to_str
-        # raises error if invalid URI
-        URI.parse(uri)
-      end
-
-      obj = new(nil, validate)
-      obj.instance_eval {
-        @reader = XML::Reader.file(uri)
-        _skip_leader
-      }
-      if block_given? then
-        begin
-          ret = yield obj
-        ensure
-          obj.close if obj and !obj.closed?
-        end
-        ret
-      else
-        obj
-      end
-    end
-
-    # Special class for closed PhyloXML::Parser object.
-    # It raises error for any methods except essential methods.
-    #
-    # Bio::PhyloXML internal use only.
-    class ClosedPhyloXMLParser #:nodoc:
-      def method_missing(*arg)
-        raise LibXML::XML::Error, 'closed PhyloXML::Parser object'
-      end
-    end #class ClosedPhyloXMLParser
-
-    # Closes the LibXML::Reader inside the object.
-    # It also closes the opened file if it is created by using
-    # Bio::PhyloXML::Parser.open method.
-    #
-    # When closed object is closed again, or closed object is used,
-    # it raises LibXML::XML::Error.
-    # ---
-    # *Returns*:: nil
-    def close
-      @reader.close
-      @reader = ClosedPhyloXMLParser.new
-      nil
-    end
-
-    # If the object is closed by using the close method or equivalent,
-    # returns true. Otherwise, returns false.
-    # ---
-    # *Returns*:: true or false
-    def closed?
-      if @reader.kind_of?(ClosedPhyloXMLParser) then
-        true
-      else
-        false
-      end
-    end
-
-    # Initializes LibXML::Reader and reads from the IO until it reaches
-    # the first phylogeny element.
-    #
-    # Create a new Bio::PhyloXML::Parser object.
-    #
-    #   p = Bio::PhyloXML::Parser.for_io($stdin)
-    #
-    # ---
-    # *Arguments*:
-    # * (required) _io_: IO object
-    # * (optional) _validate_: For IO reader, the "validate" option is ignored and no validation is executed.
-    # *Returns*:: Bio::PhyloXML::Parser object
-    def self.for_io(io, validate=true)
-      obj = new(nil, validate)
-      obj.instance_eval {
-        @reader = XML::Reader.io(io,
-                                 { :options =>
-                                   LibXML::XML::Parser::Options::NONET })
-        _skip_leader
-      }
-      obj
-    end
-
-    # (private) returns PhyloXML schema
-    def _schema
-      XML::Schema.document(XML::Document.file(File.join(File.dirname(__FILE__),'phyloxml.xsd')))
-    end
-    private :_schema
-
-    # (private) do validation
-    # ---
-    # *Arguments*:
-    # * (required) <em>data_type</em>_: :file for filename, :string for string
-    # * (required) _arg_: filename or string
-    # *Returns*:: (undefined)
-    def _validate(data_type, arg)
-      options = { :options =>
-        (LibXML::XML::Parser::Options::NOERROR |   # no error messages
-         LibXML::XML::Parser::Options::NOWARNING | # no warning messages
-         LibXML::XML::Parser::Options::NONET)      # no network access
-      }
-      case data_type
-      when :file
-        # No validation when special file e.g. FIFO (named pipe)
-        return unless File.file?(arg)
-        xml_instance = XML::Document.file(arg, options)
-      when :string
-        xml_instance = XML::Document.string(arg, options)
-      else
-        # no validation for unknown data type
-        return
-      end
-
-      schema = _schema
-      begin
-        flag = xml_instance.validate_schema(schema) do |msg, _|
-          # The document of libxml-ruby says that the block is called
-          # when validation failed, but it seems it is never called
-          # even when validation failed!
-          raise "Validation of the XML document against phyloxml.xsd schema failed. #{msg}"
-        end
-      rescue LibXML::XML::Error => evar
-        raise "Validation of the XML document against phyloxml.xsd schema failed, or XML error occurred. #{evar.message}"
-      end
-      unless flag then
-        raise "Validation of the XML document against phyloxml.xsd schema failed."
-      end
-    end
-    private :_validate
-
-    # (private) It seems that LibXML::XML::Reader reads from the network
-    # even if LibXML::XML::Parser::Options::NONET is set.
-    # So, for URI-like filename, '://' is replaced with ':/'.
-    def _secure_filename(filename)
-      # for safety, URI-like filename is checked.
-      if /\A[a-zA-Z]+\:\/\// =~ filename then
-        # for example, "http://a/b" is changed to "http:/a/b".
-        filename = filename.sub(/\:\/\//, ':/')
-      end
-      filename
-    end
-    private :_secure_filename
-
-    # (private) loops through until reaches phylogeny stuff
-    def _skip_leader
-      #loops through until reaches phylogeny stuff
-      # Have to leave this way, if accepting strings, instead of files
-      @reader.read until is_element?('phylogeny')
-      nil
-    end
-    private :_skip_leader
-
-    # Initializes LibXML::Reader and reads the PhyloXML-formatted string
-    # until it reaches the first phylogeny element.
-    #
-    # Create a new Bio::PhyloXML::Parser object.
-    #
-    #   str = File.read("./phyloxml_examples.xml")
-    #   p = Bio::PhyloXML::Parser.new(str)
-    #
-    #
-    # Deprecated usage: Reads data from a file. <em>str<em> is a filename.
-    #
-    #   p = Bio::PhyloXML::Parser.new("./phyloxml_examples.xml")
-    #
-    # Taking filename is deprecated. Use Bio::PhyloXML::Parser.open(filename).
-    # 
-    # ---
-    # *Arguments*:
-    # * (required) _str_: PhyloXML-formatted string
-    # * (optional) _validate_: Whether to validate the file against schema or not. Default value is true.
-    # *Returns*:: Bio::PhyloXML::Parser object
-    def initialize(str, validate=true)
-
-      @other = []
-
-      return unless str
-
-      # For compatibility, if filename-like string is given,
-      # treat it as a filename.
-      if /[\<\>\r\n]/ !~ str and File.exist?(str) then
-        # assume that str is filename
-        warn "Bio::PhyloXML::Parser.new(filename) is deprecated. Use Bio::PhyloXML::Parser.open(filename)."
-        filename = _secure_filename(str)
-        _validate(:file, filename) if validate
-        @reader = XML::Reader.file(filename)
-        _skip_leader
-        return
-      end
-
-      # initialize for string
-      @reader = XML::Reader.string(str,
-                                   { :options =>
-                                     LibXML::XML::Parser::Options::NONET })
-      _skip_leader
-    end
-
-
-    # Iterate through all trees in the file.
-    #
-    #  phyloxml = Bio::PhyloXML::Parser.open('example.xml')
-    #  phyloxml.each do |tree|
-    #    puts tree.name
-    #  end
-    #
-    def each
-      while tree = next_tree
-        yield tree
-      end
-    end
-
-    # Access the specified tree in the file. It parses trees until the specified
-    # tree is reached.
-    #
-    #  # Get 3rd tree in the file (starts counting from 0).
-    #  parser = PhyloXML::Parser.open('phyloxml_examples.xml')
-    #  tree = parser[2]
-    #
-    def [](i)
-      tree = nil
-      (i+1).times do
-       tree =  self.next_tree
-      end
-      return tree
-    end
-
-    # Parse and return the next phylogeny tree. If there are no more phylogeny
-    # element, nil is returned. If there is something else besides phylogeny
-    # elements, it is saved in the PhyloXML::Parser#other.
-    # 
-    #  p = Bio::PhyloXML::Parser.open("./phyloxml_examples.xml")
-    #  tree = p.next_tree
-    #
-    # ---
-    # *Returns*:: Bio::PhyloXML::Tree
-    def next_tree()
-
-      if not is_element?('phylogeny')
-        if @reader.node_type == XML::Reader::TYPE_END_ELEMENT
-          if is_end_element?('phyloxml')
-            return nil
-          else
-            @reader.read
-            @reader.read
-            if is_end_element?('phyloxml')
-              return nil
-            end
-          end
-        end        
-        # phyloxml can hold only phylogeny and "other" elements. If this is not
-        # phylogeny element then it is other. Also, "other" always comes after
-        # all phylogenies        
-        @other << parse_other        
-        #return nil for tree, since this is not valid phyloxml tree.
-        return nil
-      end
-
-      tree = Bio::PhyloXML::Tree.new
-
-      # keep track of current node in clades array/stack. Current node is the
-      # last element in the clades array
-      clades = []
-      clades.push tree
-      
-      #keep track of current edge to be able to parse branch_length tag
-      current_edge = nil
-
-      # we are going to parse clade iteratively by pointing (and changing) to
-      # the current node in the tree. Since the property element is both in
-      # clade and in the phylogeny, we need some boolean to know if we are
-      # parsing the clade (there can be only max 1 clade in phylogeny) or
-      # parsing phylogeny
-      parsing_clade = false
-
-      while not is_end_element?('phylogeny') do
-        break if is_end_element?('phyloxml')
-        
-        # parse phylogeny elements, except clade
-        if not parsing_clade
-
-          if is_element?('phylogeny')
-            @reader["rooted"] == "true" ? tree.rooted = true : tree.rooted = false
-            @reader["rerootable"] == "true" ? tree.rerootable = true : tree.rerootable = false
-            parse_attributes(tree, ["branch_length_unit", 'type'])
-          end
-
-          parse_simple_elements(tree, [ "name", 'description', "date"])
-
-          if is_element?('confidence')
-            tree.confidences << parse_confidence
-          end
-
-        end
-
-        if @reader.node_type == XML::Reader::TYPE_ELEMENT
-          case @reader.name
-          when 'clade'
-            #parse clade element
-
-            parsing_clade = true
-
-            node= Bio::PhyloXML::Node.new
-
-            branch_length = @reader['branch_length']
-
-            parse_attributes(node, ["id_source"])
-
-            #add new node to the tree
-            tree.add_node(node)
-            # The first clade will always be root since by xsd schema phyloxml can
-            # have 0 to 1 clades in it.
-            if tree.root == nil
-              tree.root = node
-            else
-              current_edge = tree.add_edge(clades[-1], node,
-                                           Bio::Tree::Edge.new(branch_length))
-            end
-            clades.push node
-            #end if clade element
-          else
-           parse_clade_elements(clades[-1], current_edge) if parsing_clade
-          end
-        end
-
-        #end clade element, go one parent up
-        if is_end_element?('clade')
-
-           #if we have reached the closing tag of the top-most clade, then our
-          # curent node should point to the root, If thats the case, we are done
-          # parsing the clade element
-          if clades[-1] == tree.root
-            parsing_clade = false
-          else
-            # set current node (clades[-1) to the previous clade in the array
-            clades.pop
-          end
-        end          
-
-        #parsing phylogeny elements
-        if not parsing_clade
-
-          if @reader.node_type == XML::Reader::TYPE_ELEMENT
-            case @reader.name
-            when 'property'
-              tree.properties << parse_property
-
-            when 'clade_relation'
-              clade_relation = CladeRelation.new
-              parse_attributes(clade_relation, ["id_ref_0", "id_ref_1", "distance", "type"])
-
-              #@ add unit test for this
-              if not @reader.empty_element?
-                @reader.read
-                if is_element?('confidence')
-                  clade_relation.confidence = parse_confidence
-                end
-              end
-              tree.clade_relations << clade_relation
-
-            when 'sequence_relation'
-              sequence_relation = SequenceRelation.new
-              parse_attributes(sequence_relation, ["id_ref_0", "id_ref_1", "distance", "type"])
-              if not @reader.empty_element?
-                @reader.read
-                if is_element?('confidence')
-                  sequence_relation.confidence = parse_confidence
-                end
-              end
-              tree.sequence_relations << sequence_relation
-            when 'phylogeny'
-              #do nothing
-            else
-              tree.other << parse_other
-              #puts "Not recognized element. #{@reader.name}"
-            end
-          end
-        end
-        # go to next element        
-        @reader.read    
-      end #end while not </phylogeny>
-      #move on to the next tag after /phylogeny which is text, since phylogeny
-      #end tag is empty element, which value is nil, therefore need to move to
-      #the next meaningful element (therefore @reader.read twice)
-      @reader.read 
-      @reader.read
-
-      return tree
-    end  
-
-    # return tree of specified name.
-    # @todo Implement this method. 
-    # def get_tree_by_name(name)
-
-#      while not is_end_element?('phyloxml')
-#        if is_element?('phylogeny')
-#          @reader.read
-#          @reader.read
-#
-#          if is_element?('name')
-#            @reader.read
-#            if @reader.value == name
-#              puts "equasl"
-#              tree = next_tree
-#              puts tree
-#            end
-#          end
-#        end
-#        @reader.read
-#      end
-#
-  #  end
-
-
-    private
-
-    ####
-    # Utility methods
-    ###
-
-    def is_element?(str)
-      @reader.node_type == XML::Reader::TYPE_ELEMENT and @reader.name == str ? true : false
-    end
-
-    def is_end_element?(str)
-      @reader.node_type==XML::Reader::TYPE_END_ELEMENT and @reader.name == str ? true : false
-    end
-
-    def has_reached_end_element?(str)
-      if not(is_end_element?(str))        
-        raise "Warning: Should have reached </#{str}> element here"
-      end
-    end
-
-    # Parses a simple XML element. for example <speciations>1</speciations>
-    # It reads in the value and assigns it to object.speciation = 1
-    # Also checks if have reached end tag (</speciations> and gives warning
-    # if not
-    def parse_simple_element(object, name)
-      if is_element?(name)
-        @reader.read
-        object.send("#{name}=", @reader.value)
-        @reader.read
-        has_reached_end_element?(name)
-      end
-    end
-
-    def parse_simple_elements(object, elements)
-      elements.each do |elmt|
-          parse_simple_element(object, elmt)
-      end      
-    end
-
-    #Parses list of attributes
-    #use for the code like: clade_relation.type = @reader["type"]
-    def parse_attributes(object, arr_of_attrs)
-      arr_of_attrs.each do |attr|
-        object.send("#{attr}=", @reader[attr])
-      end
-    end
-
-    def parse_clade_elements(current_node, current_edge)
-      #no loop inside, loop is already outside
-
-      if @reader.node_type == XML::Reader::TYPE_ELEMENT
-        case @reader.name
-        when 'branch_length'
-          # @todo add unit test for this. current_edge is nil, if the root clade
-          # has branch_length attribute. 
-          @reader.read
-          branch_length = @reader.value
-          current_edge.distance = branch_length.to_f if current_edge != nil
-          @reader.read
-        when 'width'
-          @reader.read
-          current_node.width = @reader.value
-          @reader.read
-        when  'name'
-          @reader.read
-          current_node.name = @reader.value
-          @reader.read
-        when 'events'
-          current_node.events = parse_events
-        when 'confidence'
-          current_node.confidences << parse_confidence
-        when 'sequence'
-          current_node.sequences << parse_sequence
-        when 'property'
-          current_node.properties << parse_property
-        when 'taxonomy'
-          current_node.taxonomies << parse_taxonomy
-        when 'distribution'
-          current_node.distributions << parse_distribution
-        when 'node_id'
-          id = Id.new
-          id.type = @reader["type"]
-          @reader.read
-          id.value = @reader.value
-          @reader.read
-          #has_reached_end_element?('node_id')
-          #@todo write unit test for this. There is no example of this in the example files
-          current_node.id = id
-        when 'color'
-          color = BranchColor.new
-          parse_simple_element(color, 'red')
-          parse_simple_element(color, 'green')
-          parse_simple_element(color, 'blue')
-          current_node.color = color
-          #@todo add unit test for this
-        when 'date'
-          date = Date.new
-          date.unit = @reader["unit"]
-          #move to the next token, which is always empty, since date tag does not
-          # have text associated with it
-          @reader.read
-          @reader.read #now the token is the first tag under date tag
-          while not(is_end_element?('date'))
-            parse_simple_element(date, 'desc')
-            parse_simple_element(date, 'value')
-            parse_simple_element(date, 'minimum')
-            parse_simple_element(date, 'maximum')
-            @reader.read
-          end
-          current_node.date = date
-        when 'reference'
-          reference = Reference.new()
-          reference.doi = @reader['doi']
-          if not @reader.empty_element?
-            while not is_end_element?('reference')
-              parse_simple_element(reference, 'desc')
-              @reader.read
-            end
-          end
-          current_node.references << reference
-        when 'binary_characters'
-          current_node.binary_characters  = parse_binary_characters
-        when 'clade'
-          #do nothing
-        else
-          current_node.other << parse_other
-          #puts "No match found in parse_clade_elements.(#{@reader.name})"
-        end
-
-      end
-
-    end #parse_clade_elements
-
-    def parse_events()
-      events = PhyloXML::Events.new
-      @reader.read #go to next element
-      while not(is_end_element?('events')) do
-        parse_simple_elements(events, ['type', 'duplications',
-                                            'speciations', 'losses'])
-        if is_element?('confidence')
-          events.confidence = parse_confidence
-          #@todo could add unit test for this (example file does not have this case)
-        end
-        @reader.read
-      end
-      return events
-    end #parse_events
-
-    def parse_taxonomy
-      taxonomy = PhyloXML::Taxonomy.new
-      parse_attributes(taxonomy, ["id_source"])
-      @reader.read
-      while not(is_end_element?('taxonomy')) do
-
-        if @reader.node_type == XML::Reader::TYPE_ELEMENT
-          case @reader.name
-          when 'code'
-            @reader.read
-            taxonomy.code = @reader.value
-            @reader.read
-          when 'scientific_name'
-            @reader.read
-            taxonomy.scientific_name = @reader.value
-            @reader.read
-          when 'rank'
-            @reader.read
-            taxonomy.rank = @reader.value
-            @reader.read
-          when 'authority'
-            @reader.read
-            taxonomy.authority = @reader.value
-            @reader.read
-          when 'id'
-            taxonomy.taxonomy_id = parse_id('id')
-          when 'common_name'
-            @reader.read
-            taxonomy.common_names << @reader.value
-            @reader.read
-            #has_reached_end_element?('common_name')
-          when 'synonym'
-            @reader.read
-            taxonomy.synonyms << @reader.value
-            @reader.read
-            #has_reached_end_element?('synonym')
-          when 'uri'
-            taxonomy.uri = parse_uri
-          else
-            taxonomy.other << parse_other
-          end
-        end
-
-        @reader.read  #move to next tag in the loop
-      end
-      return taxonomy
-    end #parse_taxonomy
-
-    private
-
-    def parse_sequence
-      sequence = Sequence.new
-      parse_attributes(sequence, ["type", "id_source", "id_ref"])
-      
-      @reader.read
-      while not(is_end_element?('sequence'))
-
-        if @reader.node_type == XML::Reader::TYPE_ELEMENT
-          case @reader.name
-          when 'symbol'
-            @reader.read
-            sequence.symbol = @reader.value
-            @reader.read
-          when 'name'
-            @reader.read
-            sequence.name = @reader.value
-            @reader.read
-          when 'location'
-            @reader.read
-            sequence.location = @reader.value
-            @reader.read
-          when 'mol_seq'
-            sequence.is_aligned = @reader["is_aligned"]
-            @reader.read
-            sequence.mol_seq = @reader.value
-            @reader.read
-            has_reached_end_element?('mol_seq')
-          when 'accession'
-            sequence.accession = Accession.new
-            sequence.accession.source = @reader["source"]
-            @reader.read
-            sequence.accession.value = @reader.value
-            @reader.read
-            has_reached_end_element?('accession')
-          when 'uri'
-            sequence.uri = parse_uri
-          when 'annotation'
-            sequence.annotations << parse_annotation
-          when 'domain_architecture'
-            sequence.domain_architecture = DomainArchitecture.new
-            sequence.domain_architecture.length = @reader["length"]
-            @reader.read
-            @reader.read
-            while not(is_end_element?('domain_architecture'))
-              sequence.domain_architecture.domains << parse_domain
-              @reader.read #go to next domain element
-            end
-          else
-            sequence.other << parse_other
-            #@todo add unit test            
-          end
-        end
-
-        @reader.read
-      end
-      return sequence
-    end #parse_sequence
-
-    def parse_uri
-      uri = Uri.new
-      parse_attributes(uri, ["desc", "type"])
-      parse_simple_element(uri, 'uri')
-      return uri
-    end
-
-    def parse_annotation
-      annotation = Annotation.new
-
-      parse_attributes(annotation, ['ref', 'source', 'evidence', 'type'])
-
-      if not @reader.empty_element?
-        while not(is_end_element?('annotation'))
-          parse_simple_element(annotation, 'desc') if is_element?('desc')
-
-          annotation.confidence  = parse_confidence if is_element?('confidence')
-
-          annotation.properties << parse_property if is_element?('property')
-
-          if is_element?('uri')
-            annotation.uri = parse_uri        
-          end
-
-          @reader.read
-        end
-        
-      end
-      return annotation
-    end
-
-    def parse_property
-      property = Property.new
-      parse_attributes(property, ["ref", "unit", "datatype", "applies_to", "id_ref"])
-      @reader.read
-      property.value = @reader.value
-      @reader.read
-      has_reached_end_element?('property')     
-      return property
-    end #parse_property
-
-    def parse_confidence
-      type = @reader["type"]
-      @reader.read
-      value = @reader.value.to_f
-      @reader.read
-      has_reached_end_element?('confidence')
-      return Confidence.new(type, value)
-    end #parse_confidence
-
-    def parse_distribution
-      distribution = Distribution.new
-      @reader.read
-      while not(is_end_element?('distribution')) do
-
-        parse_simple_element(distribution, 'desc')
-
-        distribution.points << parse_point if is_element?('point')
-        distribution.polygons << parse_polygon if is_element?('polygon')
-
-        @reader.read
-      end
-      return distribution
-    end #parse_distribution
-
-    def parse_point
-      point = Point.new
-
-      point.geodetic_datum = @reader["geodetic_datum"]
-      point.alt_unit = @reader["alt_unit"]
-
-      @reader.read
-      while not(is_end_element?('point')) do
-
-        parse_simple_elements(point, ['lat', 'long'] )
-
-        if is_element?('alt')
-          @reader.read
-          point.alt = @reader.value.to_f
-          @reader.read
-          has_reached_end_element?('alt')
-        end
-        #advance reader
-        @reader.read
-      end
-      return point
-    end #parse_point
-
-    def parse_polygon
-      polygon = Polygon.new
-      @reader.read
-      while not(is_end_element?('polygon')) do
-        polygon.points << parse_point if is_element?('point')
-        @reader.read
-      end
-
-      #@todo should check for it at all? Probably not if xml is valid.
-      if polygon.points.length <3
-        puts "Warning: <polygon> should have at least 3 points"
-      end
-      return polygon
-    end #parse_polygon
-
-    def parse_id(tag_name)
-      id = Id.new
-      id.provider = @reader["provider"]
-      @reader.read
-      id.value = @reader.value
-      @reader.read #@todo shouldn't there be another read?
-      has_reached_end_element?(tag_name)
-      return id
-    end #parse_id
-
-    def parse_domain
-      domain = ProteinDomain.new
-      parse_attributes(domain, ["from", "to", "confidence", "id"])
-      @reader.read
-      domain.value = @reader.value
-      @reader.read
-      has_reached_end_element?('domain')
-      @reader.read
-      return domain
-    end
-
-    def parse_binary_characters
-      b = PhyloXML::BinaryCharacters.new
-      b.bc_type = @reader['type']
-
-      parse_attributes(b, ['gained_count', 'absent_count', 'lost_count', 'present_count'])
-      if not @reader.empty_element?
-        @reader.read
-        while not is_end_element?('binary_characters')
-
-          parse_bc(b, 'lost')
-          parse_bc(b, 'gained')
-          parse_bc(b, 'absent')
-          parse_bc(b, 'present')
-
-          @reader.read
-        end
-      end
-      return b
-    end #parse_binary_characters
-
-    def parse_bc(object, element)
-      if is_element?(element)
-        @reader.read
-        while not is_end_element?(element)
-          if is_element?('bc')
-            @reader.read
-            object.send(element) << @reader.value
-            @reader.read
-            has_reached_end_element?('bc')
-          end
-        @reader.read
-        end
-      end
-    end #parse_bc
-
-    def parse_other
-      other_obj = PhyloXML::Other.new
-      other_obj.element_name = @reader.name
-      #parse attributes
-      code = @reader.move_to_first_attribute
-      while code ==1
-        other_obj.attributes[@reader.name] = @reader.value
-        code = @reader.move_to_next_attribute        
-      end
-
-      while not is_end_element?(other_obj.element_name) do
-        @reader.read
-        if @reader.node_type == XML::Reader::TYPE_ELEMENT
-           other_obj.children << parse_other #recursice call to parse children
-        elsif @reader.node_type == XML::Reader::TYPE_TEXT
-          other_obj.value = @reader.value
-        end
-      end
-      #just a check
-      has_reached_end_element?(other_obj.element_name)
-      return other_obj
-    end #parse_other
-
-  end #class phyloxmlParser
-
-end #module PhyloXML
-  
-end #module Bio