bio 1.5.2 → 1.6.0.pre.20181210

data/lib/bio/db/biosql/sequence.rb

@@ -1,444 +0,0 @@
-
-#TODO save on db reading from a genbank or embl object
-module Bio
-  class SQL
-
-
-
-    class Sequence
-      private
-      #      example
-      #      bioentry_qualifier_anchor :molecule_type, :synonym=>'mol_type'
-      #      this function creates other 3 functions, molecule_type, molecule_type=, molecule_type_update
-      #molecule_type => return an array of strings, where each string is the value associated with the qualifier, ordered by rank.
-      #molecule_type=value add a bioentry_qualifier value to the table
-      #molecule_type_update(value, rank) update an entry of the table with an existing rank
-      #the method inferr the qualifier term from the name of the first symbol, or you can specify a synonym to use
-
-      #creating an object with to_biosql is transaction safe.
-
-      #TODO: implement setting for more than a qualifier-vale.
-      def self.bioentry_qualifier_anchor(sym, *args)
-        options = args.first || Hash.new
-        #options.assert_valid_keys(:rank,:synonym,:multi)
-        method_reader = sym.to_s.to_sym
-        method_writer_operator = (sym.to_s+"=").to_sym
-        method_writer_modder = (sym.to_s+"_update").to_sym
-        synonym = options[:synonym].nil? ? sym.to_s : options[:synonym]
-
-        #DELETE        #Bio::SQL::Term.create(:name=>synonym, :ontology=> Bio::SQL::Ontology.find_by_name('Annotation Tags')) unless Bio::SQL::Term.exists?(:name =>synonym)
-        send :define_method, method_reader do
-          #return an array of bioentry_qualifier_values
-          begin
-            #DELETE            ontology_annotation_tags = Ontology.find_or_create({:name=>'Annotation Tags'})
-            term  = Term.first(:conditions=>["name = ?",synonym]) || Term.create({:name => synonym, :ontology=> Ontology.first(:conditions=>["name = ?",'Annotation Tags'])})
-            bioentry_qualifier_values = @entry.bioentry_qualifier_values.all(:conditions=>["term_id = ?",term.term_id])
-            data = bioentry_qualifier_values.map{|row| row.value} unless bioentry_qualifier_values.nil?
-            begin
-              # this block try to check if the data retrived is a
-              # Date or not and change it according to GenBank/EMBL format
-              # in that case return a string
-              # otherwise the []
-              Date.parse(data.to_s).strftime("%d-%b-%Y").upcase
-            rescue ArgumentError, TypeError, NoMethodError, NameError
-              data
-            end
-          rescue Exception => e
-            puts "Reader Error: #{synonym} #{e.message}"
-          end
-        end
-
-        send :define_method, method_writer_operator do |value|
-          begin
-            #DELETE            ontology_annotation_tags = Ontology.find_or_create({:name=>'Annotation Tags'})
-            term  = Term.first(:conditions=>["name = ?",synonym]) || Term.create({:name => synonym, :ontology=> Ontology.first(:conditions=>["name = ?",'Annotation Tags'])})
-            datas = @entry.bioentry_qualifier_values.all(:conditions=>["term_id = ?",term.term_id])
-            #add an element incrementing the rank or setting the first to 1
-            be_qu_va=@entry.bioentry_qualifier_values.build({:term=>term, :rank=>(datas.empty? ? 1 : datas.last.rank.succ), :value=>value})
-            be_qu_va.save
-          rescue Exception => e
-            puts "WriterOperator= Error: #{synonym} #{e.message}"
-          end
-        end
-
-        send :define_method, method_writer_modder do |value, rank|
-          begin
-            #DELETE            ontology_annotation_tags = Ontology.find_or_create({:name=>'Annotation Tags'})
-            term  = Term.first(:conditions=>["name = ?",synonym]) || Term.create({:name => synonym, :ontology=> Ontology.first(:conditions=>["name = ?",'Annotation Tags'])})
-            data = @entry.bioentry_qualifier_values.all(:term_id=>term.term_id, :rank=>rank)
-            if data.nil?
-              send method_writer_operator, value
-            else
-              data.value=value
-              data.save
-            end
-          rescue Exception => e
-            puts "WriterModder Error: #{synonym} #{e.message}"
-          end
-        end
-
-      end
-
-      public
-      attr_reader :entry
-
-      def delete
-        #TODO: check is references connected to this bioentry are leaf or not.
-        #actually I think it should be more sofisticated, check if there are
-        #other bioentries connected to references; if not delete 'em
-        @entry.references.each { |ref| ref.delete if ref.bioentries.size==1}
-        @entry.destroy
-      end
-
-      def get_seqfeature(sf)
-
-        #in seqfeature BioSQL class
-        locations_str = sf.locations.map{|loc| loc.to_s}.join(',')
-        #pp sf.locations.inspect
-        locations_str = "join(#{locations_str})" if sf.locations.count>1
-        Bio::Feature.new(sf.type_term.name, locations_str,sf.seqfeature_qualifier_values.collect{|sfqv| Bio::Feature::Qualifier.new(sfqv.term.name,sfqv.value)})
-      end
-
-      def length=(len)
-        @entry.biosequence.length=len
-      end
-
-      def initialize(options={})
-        #options.assert_valid_keys(:entry, :biodatabase,:biosequence)
-        return @entry = options[:entry] unless options[:entry].nil?
-
-        return to_biosql(options[:biosequence], options[:biodatabase]) unless options[:biosequence].nil? or options[:biodatabase].nil?
-
-      end
-
-      def to_biosql(bs,biodatabase)
-        #DELETE        #Transcaction works greatly!!!
-        begin
-          #DELETE          Bioentry.transaction do
-          @entry = biodatabase.bioentries.build({:name=>bs.entry_id})
-
-          puts "primary" if $DEBUG
-          self.primary_accession = bs.primary_accession
-
-          puts "def" if $DEBUG
-          self.definition = bs.definition unless bs.definition.nil?
-
-          puts "seqver" if $DEBUG
-          self.sequence_version = bs.sequence_version || 0
-
-          puts "divi" if $DEBUG
-          self.division = bs.division unless bs.division.nil?
-
-          puts "identifier" if $DEBUG
-          self.identifier = bs.other_seqids.collect{|dblink| "#{dblink.database}:#{dblink.id}"}.join(';') unless bs.other_seqids.nil?
-          @entry.save
-          puts "secacc" if $DEBUG
-
-          bs.secondary_accessions.each do |sa|
-            puts "#{sa}" if $DEBUG
-            #write as qualifier every secondary accession into the array
-            self.secondary_accessions = sa
-          end unless bs.secondary_accessions.nil?
-
-
-          #to create the sequence entry needs to exists
-          puts "seq" if $DEBUG
-          puts bs.seq if $DEBUG
-          self.seq = bs.seq unless bs.seq.nil?
-          puts "mol" if $DEBUG
-
-          self.molecule_type = bs.molecule_type unless bs.molecule_type.nil?
-          puts "dc" if $DEBUG
-
-          self.data_class = bs.data_class unless bs.data_class.nil?
-          puts "top" if $DEBUG
-          self.topology = bs.topology unless bs.topology.nil?
-          puts "datec" if $DEBUG
-          self.date_created = bs.date_created unless bs.date_created.nil?
-          puts "datemod" if $DEBUG
-          self.date_modified = bs.date_modified unless bs.date_modified.nil?
-          puts "key" if $DEBUG
-
-          bs.keywords.each do |kw|
-            #write as qualifier every secondary accessions into the array
-            self.keywords = kw
-          end unless bs.keywords.nil?
-
-          puts "spec" if $DEBUG
-          #self.species = bs.species unless bs.species.nil?
-          self.species = bs.species unless bs.species.empty?
-          puts "Debug: #{bs.species}" if $DEBUG
-          puts "Debug: feat..start" if $DEBUG
-
-          bs.features.each do |feat|
-            self.feature=feat
-          end unless bs.features.nil?
-
-          puts "Debug: feat...end" if $DEBUG
-          bs.references.each do |reference|
-            self.reference=reference
-          end unless bs.references.nil?
-
-          bs.comments.each do |comment|
-            self.comment=comment
-          end unless bs.comments.nil?
-
-          #DELETE          end #transaction
-          return self
-        rescue Exception => e
-          puts "to_biosql exception: #{e}"
-          puts $!
-        end #rescue
-      end #to_biosql
-
-
-      def name
-        @entry.name
-      end
-      alias entry_id name
-
-      def name=(value)
-        @entry.name=value
-      end
-      alias entry_id= name=
-
-      def primary_accession
-        @entry.accession
-      end
-
-      def primary_accession=(value)
-        @entry.accession=value
-      end
-
-      #TODO      def secondary_accession
-      #        @entry.bioentry_qualifier_values
-      #      end
-
-      def organism
-        @entry.taxon.nil? ? "" : "#{@entry.taxon.taxon_scientific_name.name}"+ (@entry.taxon.taxon_genbank_common_name ? "(#{@entry.taxon.taxon_genbank_common_name.name})" : '')
-      end
-      alias species organism
-
-      def organism=(value)
-        #FIX there is a shortcut
-        taxon_name=TaxonName.first(:conditions=>["name = ? and name_class = ?",value.gsub(/\s+\(.+\)/,''),'scientific name'])
-        if taxon_name.nil?
-          puts "Error value doesn't exists in taxon_name table with scientific name constraint."
-        else
-          @entry.taxon_id=taxon_name.taxon_id
-          @entry.save
-        end
-      end
-      alias species= organism=
-
-      def database
-        @entry.biodatabase.name
-      end
-
-      def database_desc
-        @entry.biodatabase.description
-      end
-
-      def version
-        @entry.version
-      end
-      alias sequence_version version
-
-      def version=(value)
-        @entry.version=value
-      end
-      alias sequence_version= version=
-
-      def division
-        @entry.division
-      end
-
-      def division=(value)
-        @entry.division=value
-      end
-
-      def description
-        @entry.description
-      end
-      alias definition description
-
-      def description=(value)
-        @entry.description=value
-      end
-      alias definition= description=
-
-      def identifier
-        @entry.identifier
-      end
-      alias other_seqids identifier
-
-      def identifier=(value)
-        @entry.identifier=value
-      end
-
-      bioentry_qualifier_anchor :data_class
-      bioentry_qualifier_anchor :molecule_type, :synonym=>'mol_type'
-      bioentry_qualifier_anchor :topology
-      bioentry_qualifier_anchor :date_created
-      bioentry_qualifier_anchor :date_modified, :synonym=>'date_changed'
-      bioentry_qualifier_anchor :keywords, :synonym=>'keyword'
-      bioentry_qualifier_anchor :secondary_accessions, :synonym=>'secondary_accession'
-
-      def features
-        @entry.seqfeatures.collect do |sf|
-          self.get_seqfeature(sf)
-        end
-      end
-
-      def feature=(feat)
-        #ToDo: avoid Ontology find here, probably more efficient create class variables
-        #DELETE        type_term_ontology = Ontology.find_or_create({:name=>'SeqFeature Keys'})
-        puts "feature:type_term = #{feat.feature}" if $DEBUG
-        type_term = Term.first(:conditions=>["name = ?", feat.feature]) || Term.create({:name=>feat.feature, :ontology=>Ontology.first(:conditions=>["name = ?",'SeqFeature Keys'])})
-        #DELETE        source_term_ontology = Ontology.find_or_create({:name=>'SeqFeature Sources'})
-        puts "feature:source_term" if $DEBUG
-        source_term = Term.first(:conditions=>["name = ?",'EMBLGenBankSwit'])
-        puts "feature:seqfeature" if $DEBUG
-        seqfeature = @entry.seqfeatures.build({:source_term=>source_term, :type_term=>type_term, :rank=>@entry.seqfeatures.count.succ, :display_name=>''})
-        seqfeature.save
-        puts "feature:location" if $DEBUG
-        feat.locations.each do |loc|
-          location = seqfeature.locations.build({:seqfeature=>seqfeature, :start_pos=>loc.from, :end_pos=>loc.to, :strand=>loc.strand, :rank=>seqfeature.locations.count.succ})
-          location.save
-        end
-
-        #DELETE        qual_term_ontology = Ontology.find_or_create({:name=>'Annotation Tags'})
-
-        puts "feature:qualifier" if $DEBUG
-        feat.each do |qualifier|
-          #DELETE          qual_term = Term.find_or_create({:name=>qualifier.qualifier}, {:ontology=>qual_term_ontology})
-          qual_term = Term.first(:conditions=>["name = ?", qualifier.qualifier]) || Term.create({:name=>qualifier.qualifier, :ontology=>Ontology.first(:conditions=>["name = ?", 'Annotation Tags'])})
-          qual = seqfeature.seqfeature_qualifier_values.build({:seqfeature=>seqfeature, :term=>qual_term, :value=>qualifier.value.to_s, :rank=>seqfeature.seqfeature_qualifier_values.count.succ})
-          qual.save
-
-        end
-      end
-
-      #return the seqfeature mapped from BioSQL with a type_term like 'CDS'
-      def cdsfeatures
-        @entry.cdsfeatures
-      end
-
-      # Returns the sequence.
-      # Returns a Bio::Sequence::Generic object.
-
-      def seq
-        s = @entry.biosequence
-        Bio::Sequence::Generic.new(s ? s.seq : '')
-      end
-
-      def seq=(value)
-        #TODO: revise this piece of code.
-        #chk which type of alphabet is, NU/NA/nil
-        if @entry.biosequence.nil?
-          #DELETE          puts "intoseq1"
-          @entry.biosequence = Biosequence.new(:seq=>value)
-          #          biosequence = @entry.biosequence.build({:seq=>value})
-          @entry.biosequence.save
-          #          biosequence.save
-        else
-          @entry.biosequence.seq=value
-        end
-        self.length=value.length
-        #DELETE        #@entry.biosequence.length=value.length
-        #DELETE        #break
-        @entry.save
-      end
-
-      #report parents and exclude info with "no rank". Now I report rank == class but ... Question ? Have to be reported taxonomy with rank=="class"?
-      def taxonomy
-        tax = []
-        taxon = Taxon.first(:conditions=>["taxon_id = ?",@entry.taxon.parent_taxon_id])
-        while taxon and taxon.taxon_id != taxon.parent_taxon_id and taxon.node_rank!='no rank'
-          tax << taxon.taxon_scientific_name.name if taxon.node_rank!='class'
-          #Note: I don't like this call very much, correct with a relationship in the ref class.
-          taxon = Taxon.first(:conditions=>["taxon_id = ?",taxon.parent_taxon_id])
-        end
-        tax.reverse
-      end
-
-      def length
-        @entry.biosequence.length
-      end
-
-      def references
-        #return and array of hash, hash has these keys ["title", "dbxref_id", "reference_id", "authors", "crc", "location"]
-        #probably would be better to d a class refrence to collect these informations
-        @entry.bioentry_references.collect do |bio_ref|
-          hash = Hash.new
-          hash['authors'] = bio_ref.reference.authors.gsub(/\.\s/, "\.\s\|").split(/\|/) if (bio_ref.reference and bio_ref.reference.authors)
-
-          hash['sequence_position'] = "#{bio_ref.start_pos}-#{bio_ref.end_pos}" if (bio_ref.start_pos and bio_ref.end_pos)
-          hash['title'] = bio_ref.reference.title
-          hash['embl_gb_record_number'] = bio_ref.rank
-          #TODO: solve the problem with specific comment per reference.
-          #TODO: get dbxref
-          #take a look when location is build up in def reference=(value)
-
-          bio_ref.reference.location.split('|').each do |element|
-            key,value=element.split('=')
-            hash[key]=value
-          end unless bio_ref.reference.location.nil?
-
-          hash['xrefs'] = bio_ref.reference.dbxref ? "#{bio_ref.reference.dbxref.dbname}; #{bio_ref.reference.dbxref.accession}." : ''
-          Bio::Reference.new(hash)
-        end
-      end
-
-      def comments
-        @entry.comments.map do |comment|
-          comment.comment_text
-        end
-      end
-
-      def reference=(value)       
-        locations=Array.new
-        locations << "journal=#{value.journal}" unless value.journal.empty?
-        locations << "volume=#{value.volume}" unless value.volume.empty?
-        locations << "issue=#{value.issue}" unless value.issue.empty?
-        locations << "pages=#{value.pages}" unless value.pages.empty?
-        locations << "year=#{value.year}" unless value.year.empty?
-        locations << "pubmed=#{value.pubmed}" unless value.pubmed.empty?
-        locations << "medline=#{value.medline}" unless value.medline.empty?
-        locations << "doi=#{value.doi}" unless value.doi.nil?
-        locations << "abstract=#{value.abstract}" unless value.abstract.empty?
-        locations << "url=#{value.url}" unless value.url.nil?
-        locations << "mesh=#{value.mesh}" unless value.mesh.empty?
-        locations << "affiliations=#{value.affiliations}" unless value.affiliations.empty?
-        locations << "comments=#{value.comments.join('~')}"unless value.comments.nil?
-        start_pos, end_pos = value.sequence_position ? value.sequence_position.gsub(/\s*/,'').split('-') : [nil,nil]
-        reference= Reference.first(:conditions=>["title = ?",value.title]) || Reference.create({:title=>value.title,:authors=>value.authors.join(' '), :location=>locations.join('|')})
-        bio_reference=@entry.bioentry_references.build({:reference=>reference,:rank=>value.embl_gb_record_number, :start_pos=>start_pos, :end_pos=>end_pos})
-        bio_reference.save
-      end
-
-      def comment=(value)
-        #DELETE        comment=Comment.new({:bioentry=>@entry, :comment_text=>value, :rank=>@entry.comments.count.succ})
-        comment = @entry.comments.build({:comment_text=>value, :rank=>@entry.comments.count.succ})
-        comment.save
-      end
-
-      def save
-        #I should add chks for SQL errors
-        @entry.biosequence.save
-        @entry.save
-      end
-      def to_fasta
-        ">" + accession + "\n" + seq.gsub(Regexp.new(".{1,#{60}}"), "\\0\n")
-      end
-
-      def to_fasta_reverse_complememt
-        ">" + accession + "\n" + seq.reverse_complement.gsub(Regexp.new(".{1,#{60}}"), "\\0\n")
-      end
-
-      def to_biosequence
-        Bio::Sequence.adapter(self,Bio::Sequence::Adapter::BioSQL)
-      end
-    end #Sequence
-  end #SQL
-end #Bio

data/lib/bio/db/phyloxml/phyloxml.xsd

@@ -1,582 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--                                                             -->
-<!-- phyloXML                                                    -->
-<!--                                                             -->
-<!-- schema in XMLSchema                                         -->
-<!--                                                             -->
-<!-- License: The phyloXML XML Schema Definition is              -->
-<!--          dual-licensed under the LGPL or Ruby's             -->
-<!--          License.                                           -->
-<!--          You can redistribute and/or modify                 -->
-<!--          it under either the terms of the LGPL,             -->
-<!--          or Ruby's License.                                 -->
-<!--          see: http://www.ruby-lang.org/en/about/license.txt -->
-<!--                                                             -->
-<!-- Copyright (c) 2008-2009 Christian M Zmasek                  -->
-<!--                                                             -->
-<!-- www.phyloxml.org                                            -->
-<!-- Version: 1.10                                               -->
-<!-- Last modified: 2009.11.17 by Christian M Zmasek             -->
-<!--                                                             -->
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:phy="http://www.phyloxml.org"
-   targetNamespace="http://www.phyloxml.org" elementFormDefault="qualified" attributeFormDefault="unqualified">
-   <xs:annotation>
-      <xs:documentation> phyloXML is an XML language to describe evolutionary trees and associated data. Version: 1.10.
-         License: dual-licensed under the LGPL or Ruby's License. Copyright (c) 2008-2009 Christian M Zmasek.</xs:documentation>
-   </xs:annotation>
-   <!-- phyloxml is the root element:-->
-   <xs:element name="phyloxml" type="phy:Phyloxml"/>
-   <!-- phyloXML definition:-->
-   <xs:complexType name="Phyloxml">
-      <xs:annotation>
-         <xs:documentation> 'phyloxml' is the name of the root element. Phyloxml contains an arbitrary number of
-            'phylogeny' elements (each representing one phylogeny) possibly followed by elements from other namespaces.
-         </xs:documentation>
-      </xs:annotation>
-      <xs:sequence maxOccurs="unbounded">
-         <xs:element name="phylogeny" type="phy:Phylogeny" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
-      </xs:sequence>
-   </xs:complexType>
-   <!-- Phylogeny:-->
-   <xs:complexType name="Phylogeny">
-      <xs:annotation>
-         <xs:documentation> Element Phylogeny is used to represent a phylogeny. The required attribute 'rooted' is used
-            to indicate whether the phylogeny is rooted or not. The attribute 'rerootable' 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). The attribute 'type' can be used to indicate the type of phylogeny (i.e.
-            'gene tree'). It is recommended to use the attribute 'branch_length_unit' if the phylogeny has branch
-            lengths. Element clade is used in a recursive manner to describe the topology of a phylogenetic
-         tree.</xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="name" type="xs:token" minOccurs="0"/>
-         <xs:element name="id" type="phy:Id" minOccurs="0"/>
-         <xs:element name="description" type="xs:token" minOccurs="0"/>
-         <xs:element name="date" type="xs:dateTime" minOccurs="0"/>
-         <xs:element name="confidence" type="phy:Confidence" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:element name="clade" type="phy:Clade" minOccurs="0"/>
-         <xs:element name="clade_relation" type="phy:CladeRelation" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:element name="sequence_relation" type="phy:SequenceRelation" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:element name="property" type="phy:Property" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
-      </xs:sequence>
-      <xs:attribute name="rooted" type="xs:boolean" use="required"/>
-      <xs:attribute name="rerootable" type="xs:boolean"/>
-      <xs:attribute name="branch_length_unit" type="xs:token"/>
-      <xs:attribute name="type" type="xs:token"/>
-   </xs:complexType>
-   <!-- Clade:-->
-   <xs:complexType name="Clade">
-      <xs:annotation>
-         <xs:documentation> Element Clade is used in a recursive manner to describe the topology of a phylogenetic tree.
-            The parent branch length of a clade can be described either with the 'branch_length' element or the
-            'branch_length' attribute (it is not recommended to use both at the same time, though). Usage of the
-            'branch_length' attribute allows for a less verbose description. Element 'confidence' is used to indicate
-            the support for a clade/parent branch. Element 'events' is used to describe such events as gene-duplications
-            at the root node/parent branch of a clade. Element 'width' is the branch width for this clade (including
-            parent branch). Both 'color' and 'width' elements apply for the whole clade unless overwritten in-sub
-            clades. Attribute 'id_source' is used to link other elements to a clade (on the xml-level).
-         </xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="name" type="xs:token" minOccurs="0"/>
-         <xs:element name="branch_length" type="xs:double" minOccurs="0"/>
-         <xs:element name="confidence" type="phy:Confidence" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:element name="width" type="xs:double" minOccurs="0"/>
-         <xs:element name="color" type="phy:BranchColor" minOccurs="0"/>
-         <xs:element name="node_id" type="phy:Id" minOccurs="0"/>
-         <xs:element name="taxonomy" type="phy:Taxonomy" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:element name="sequence" type="phy:Sequence" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:element name="events" type="phy:Events" minOccurs="0"/>
-         <xs:element name="binary_characters" type="phy:BinaryCharacters" minOccurs="0"/>
-         <xs:element name="distribution" type="phy:Distribution" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:element name="date" type="phy:Date" minOccurs="0"/>
-         <xs:element name="reference" type="phy:Reference" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:element name="property" type="phy:Property" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:element name="clade" type="phy:Clade" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
-      </xs:sequence>
-      <xs:attribute name="branch_length" type="xs:double"/>
-      <xs:attribute name="id_source" type="phy:id_source"/>
-   </xs:complexType>
-   <!-- Taxonomy:-->
-   <xs:complexType name="Taxonomy">
-      <xs:annotation>
-         <xs:documentation> Element Taxonomy is used to describe taxonomic information for a clade. Element 'code' is
-            intended to store UniProt/Swiss-Prot style organism codes (e.g. 'APLCA' for the California sea hare 'Aplysia
-            californica') or other styles of mnemonics (e.g. 'Aca'). Element 'authority' is used to keep the authority,
-            such as 'J. G. Cooper, 1863', associated with the 'scientific_name'. Element 'id' is used for a unique
-            identifier of a taxon (for example '6500' with 'ncbi_taxonomy' as 'provider' for the California sea hare).
-            Attribute 'id_source' is used to link other elements to a taxonomy (on the xml-level).</xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="id" type="phy:Id" minOccurs="0"/>
-         <xs:element name="code" type="phy:TaxonomyCode" minOccurs="0"/>
-         <xs:element name="scientific_name" type="xs:token" minOccurs="0"/>
-         <xs:element name="authority" type="xs:token" minOccurs="0"/>
-         <xs:element name="common_name" type="xs:token" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:element name="synonym" type="xs:token" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:element name="rank" type="phy:Rank" minOccurs="0"/>
-         <xs:element name="uri" type="phy:Uri" minOccurs="0"/>
-         <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
-      </xs:sequence>
-      <xs:attribute name="id_source" type="phy:id_source"/>
-   </xs:complexType>
-   <xs:simpleType name="TaxonomyCode">
-      <xs:restriction base="xs:token">
-         <xs:pattern value="[a-zA-Z0-9_]{2,10}"/>
-      </xs:restriction>
-   </xs:simpleType>
-   <xs:simpleType name="Rank">
-      <xs:restriction base="xs:token">
-         <xs:enumeration value="domain"/>
-         <xs:enumeration value="kingdom"/>
-         <xs:enumeration value="subkingdom"/>
-         <xs:enumeration value="branch"/>
-         <xs:enumeration value="infrakingdom"/>
-         <xs:enumeration value="superphylum"/>
-         <xs:enumeration value="phylum"/>
-         <xs:enumeration value="subphylum"/>
-         <xs:enumeration value="infraphylum"/>
-         <xs:enumeration value="microphylum"/>
-         <xs:enumeration value="superdivision"/>
-         <xs:enumeration value="division"/>
-         <xs:enumeration value="subdivision"/>
-         <xs:enumeration value="infradivision"/>
-         <xs:enumeration value="superclass"/>
-         <xs:enumeration value="class"/>
-         <xs:enumeration value="subclass"/>
-         <xs:enumeration value="infraclass"/>
-         <xs:enumeration value="superlegion"/>
-         <xs:enumeration value="legion"/>
-         <xs:enumeration value="sublegion"/>
-         <xs:enumeration value="infralegion"/>
-         <xs:enumeration value="supercohort"/>
-         <xs:enumeration value="cohort"/>
-         <xs:enumeration value="subcohort"/>
-         <xs:enumeration value="infracohort"/>
-         <xs:enumeration value="superorder"/>
-         <xs:enumeration value="order"/>
-         <xs:enumeration value="suborder"/>
-         <xs:enumeration value="superfamily"/>
-         <xs:enumeration value="family"/>
-         <xs:enumeration value="subfamily"/>
-         <xs:enumeration value="supertribe"/>
-         <xs:enumeration value="tribe"/>
-         <xs:enumeration value="subtribe"/>
-         <xs:enumeration value="infratribe"/>
-         <xs:enumeration value="genus"/>
-         <xs:enumeration value="subgenus"/>
-         <xs:enumeration value="superspecies"/>
-         <xs:enumeration value="species"/>
-         <xs:enumeration value="subspecies"/>
-         <xs:enumeration value="variety"/>
-         <xs:enumeration value="subvariety"/>
-         <xs:enumeration value="form"/>
-         <xs:enumeration value="subform"/>
-         <xs:enumeration value="cultivar"/>
-         <xs:enumeration value="unknown"/>
-         <xs:enumeration value="other"/>
-      </xs:restriction>
-   </xs:simpleType>
-   <!-- Sequence:-->
-   <xs:complexType name="Sequence">
-      <xs:annotation>
-         <xs:documentation> Element Sequence is used to represent a molecular sequence (Protein, DNA, RNA) associated
-            with a node. 'symbol' is a short (maximal ten characters) symbol of the sequence (e.g. 'ACTM') whereas
-            'name' is used for the full name (e.g. 'muscle Actin'). 'location' is used for the location of a sequence on
-            a genome/chromosome. The actual sequence can be stored with the 'mol_seq' element. Attribute 'type' is used
-            to indicate the type of sequence ('dna', 'rna', or 'protein'). One intended use for 'id_ref' is to link a
-            sequence to a taxonomy (via the taxonomy's 'id_source') in case of multiple sequences and taxonomies per
-            node. </xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="symbol" type="phy:SequenceSymbol" minOccurs="0"/>
-         <xs:element name="accession" type="phy:Accession" minOccurs="0"/>
-         <xs:element name="name" type="xs:token" minOccurs="0"/>
-         <xs:element name="location" type="xs:token" minOccurs="0"/>
-         <xs:element name="mol_seq" type="phy:MolSeq" minOccurs="0"/>
-         <xs:element name="uri" type="phy:Uri" minOccurs="0"/>
-         <xs:element name="annotation" type="phy:Annotation" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:element name="domain_architecture" type="phy:DomainArchitecture" minOccurs="0"/>
-         <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
-      </xs:sequence>
-      <xs:attribute name="type" type="phy:SequenceType"/>
-      <xs:attribute name="id_source" type="phy:id_source"/>
-      <xs:attribute name="id_ref" type="phy:id_ref"/>
-   </xs:complexType>
-   <xs:simpleType name="SequenceSymbol">
-      <xs:restriction base="xs:token">
-         <xs:pattern value="\S{1,10}"/>
-      </xs:restriction>
-   </xs:simpleType>
-   <xs:complexType name="MolSeq">
-      <xs:annotation>
-         <xs:documentation> Element 'mol_seq' is used to store molecular sequences. The 'is_aligned' attribute is 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).</xs:documentation>
-      </xs:annotation>
-      <xs:simpleContent>
-         <xs:extension base="phy:MolSeqChars">
-            <xs:attribute name="is_aligned" type="xs:boolean"/>
-         </xs:extension>
-      </xs:simpleContent>
-   </xs:complexType>
-   <xs:simpleType name="MolSeqChars">
-      <xs:restriction base="xs:token">
-         <xs:pattern value="[a-zA-Z\.\-\?\*_]+"/>
-      </xs:restriction>
-   </xs:simpleType>
-   <xs:simpleType name="SequenceType">
-      <xs:restriction base="xs:token">
-         <xs:enumeration value="rna"/>
-         <xs:enumeration value="dna"/>
-         <xs:enumeration value="protein"/>
-      </xs:restriction>
-   </xs:simpleType>
-   <!-- Accession:-->
-   <xs:complexType name="Accession">
-      <xs:annotation>
-         <xs:documentation> Element Accession is used to capture the local part in a sequence identifier (e.g. 'P17304'
-            in 'UniProtKB:P17304', in which case the 'source' attribute would be 'UniProtKB'). </xs:documentation>
-      </xs:annotation>
-      <xs:simpleContent>
-         <xs:extension base="xs:token">
-            <xs:attribute name="source" type="xs:token" use="required"/>
-         </xs:extension>
-      </xs:simpleContent>
-   </xs:complexType>
-   <!-- DomainArchitecture: -->
-   <xs:complexType name="DomainArchitecture">
-      <xs:annotation>
-         <xs:documentation> This is used describe the domain architecture of a protein. Attribute 'length' is the total
-            length of the protein</xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="domain" type="phy:ProteinDomain" minOccurs="1" maxOccurs="unbounded"/>
-      </xs:sequence>
-      <xs:attribute name="length" type="xs:nonNegativeInteger"/>
-   </xs:complexType>
-   <xs:complexType name="ProteinDomain">
-      <xs:annotation>
-         <xs:documentation> To represent an individual domain in a domain architecture. The name/unique identifier is
-            described via the 'id' attribute. 'confidence' can be used to store (i.e.) E-values.</xs:documentation>
-      </xs:annotation>
-      <xs:simpleContent>
-         <xs:extension base="xs:token">
-            <xs:attribute name="from" type="xs:nonNegativeInteger" use="required"/>
-            <xs:attribute name="to" type="xs:nonNegativeInteger" use="required"/>
-            <xs:attribute name="confidence" type="xs:double"/>
-            <xs:attribute name="id" type="xs:token"/>
-         </xs:extension>
-      </xs:simpleContent>
-   </xs:complexType>
-   <!-- Events:-->
-   <xs:complexType name="Events">
-      <xs:annotation>
-         <xs:documentation> Events at the root node of a clade (e.g. one gene duplication). </xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="type" type="phy:EventType" minOccurs="0"/>
-         <xs:element name="duplications" type="xs:nonNegativeInteger" minOccurs="0"/>
-         <xs:element name="speciations" type="xs:nonNegativeInteger" minOccurs="0"/>
-         <xs:element name="losses" type="xs:nonNegativeInteger" minOccurs="0"/>
-         <xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
-      </xs:sequence>
-   </xs:complexType>
-   <xs:simpleType name="EventType">
-      <xs:restriction base="xs:token">
-         <xs:enumeration value="transfer"/>
-         <xs:enumeration value="fusion"/>
-         <xs:enumeration value="speciation_or_duplication"/>
-         <xs:enumeration value="other"/>
-         <xs:enumeration value="mixed"/>
-         <xs:enumeration value="unassigned"/>
-      </xs:restriction>
-   </xs:simpleType>
-   <!--BinaryCharacters:-->
-   <xs:complexType name="BinaryCharacters">
-      <xs:annotation>
-         <xs:documentation> The names and/or counts of binary characters present, gained, and lost at the root of a
-            clade. </xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="gained" type="phy:BinaryCharacterList" minOccurs="0"/>
-         <xs:element name="lost" type="phy:BinaryCharacterList" minOccurs="0"/>
-         <xs:element name="present" type="phy:BinaryCharacterList" minOccurs="0"/>
-         <xs:element name="absent" type="phy:BinaryCharacterList" minOccurs="0"/>
-      </xs:sequence>
-      <xs:attribute name="type" type="xs:token"/>
-      <xs:attribute name="gained_count" type="xs:nonNegativeInteger"/>
-      <xs:attribute name="lost_count" type="xs:nonNegativeInteger"/>
-      <xs:attribute name="present_count" type="xs:nonNegativeInteger"/>
-      <xs:attribute name="absent_count" type="xs:nonNegativeInteger"/>
-   </xs:complexType>
-   <xs:complexType name="BinaryCharacterList">
-      <xs:sequence>
-         <xs:element name="bc" type="xs:token" maxOccurs="unbounded"/>
-      </xs:sequence>
-   </xs:complexType>
-   <!-- Reference:-->
-   <xs:complexType name="Reference">
-      <xs:annotation>
-         <xs:documentation> A literature reference for a clade. It is recommended to use the 'doi' attribute instead of
-            the free text 'desc' element whenever possible. </xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="desc" type="xs:token" minOccurs="0"/>
-      </xs:sequence>
-      <xs:attribute name="doi" type="phy:Doi"/>
-   </xs:complexType>
-   <xs:simpleType name="Doi">
-      <xs:restriction base="xs:token">
-         <xs:pattern value="[a-zA-Z0-9_\.]+/\S+"/>
-      </xs:restriction>
-   </xs:simpleType>
-   <!-- Annotation:-->
-   <xs:complexType name="Annotation">
-      <xs:annotation>
-         <xs:documentation> 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'). Optional element 'desc' allows for a free text
-            description. Optional element 'confidence' is used to state the type and value of support for a annotation.
-            Similarly, optional attribute 'evidence' is used to describe the evidence for a annotation as free text
-            (e.g. 'experimental'). Optional element 'property' allows for further, typed and referenced annotations from
-            external resources.</xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="desc" type="xs:token" minOccurs="0"/>
-         <xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
-         <xs:element name="property" type="phy:Property" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:element name="uri" type="phy:Uri" minOccurs="0"/>
-      </xs:sequence>
-      <xs:attribute name="ref" type="phy:ref"/>
-      <xs:attribute name="source" type="xs:token"/>
-      <xs:attribute name="evidence" type="xs:token"/>
-      <xs:attribute name="type" type="xs:token"/>
-   </xs:complexType>
-   <!-- Property:-->
-   <xs:complexType name="Property" mixed="true">
-      <xs:annotation>
-         <xs:documentation> 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: &lt;property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade"
-            unit="METRIC:m"&gt; 200 &lt;/property&gt; </xs:documentation>
-      </xs:annotation>
-      <xs:attribute name="ref" type="phy:ref" use="required"/>
-      <xs:attribute name="unit" type="phy:ref"/>
-      <xs:attribute name="datatype" type="phy:PropertyDataType" use="required"/>
-      <xs:attribute name="applies_to" type="phy:AppliesTo" use="required"/>
-      <xs:attribute name="id_ref" type="phy:id_ref"/>
-   </xs:complexType>
-   <xs:simpleType name="ref">
-      <xs:restriction base="xs:token">
-         <xs:pattern value="[a-zA-Z0-9_]+:[a-zA-Z0-9_\.\-\s]+"/>
-      </xs:restriction>
-   </xs:simpleType>
-   <xs:simpleType name="AppliesTo">
-      <xs:restriction base="xs:token">
-         <xs:enumeration value="phylogeny"/>
-         <xs:enumeration value="clade"/>
-         <xs:enumeration value="node"/>
-         <xs:enumeration value="annotation"/>
-         <xs:enumeration value="parent_branch"/>
-         <xs:enumeration value="other"/>
-      </xs:restriction>
-   </xs:simpleType>
-   <xs:simpleType name="PropertyDataType">
-      <xs:restriction base="xs:token">
-         <xs:enumeration value="xsd:string"/>
-         <xs:enumeration value="xsd:boolean"/>
-         <xs:enumeration value="xsd:decimal"/>
-         <xs:enumeration value="xsd:float"/>
-         <xs:enumeration value="xsd:double"/>
-         <xs:enumeration value="xsd:duration"/>
-         <xs:enumeration value="xsd:dateTime"/>
-         <xs:enumeration value="xsd:time"/>
-         <xs:enumeration value="xsd:date"/>
-         <xs:enumeration value="xsd:gYearMonth"/>
-         <xs:enumeration value="xsd:gYear"/>
-         <xs:enumeration value="xsd:gMonthDay"/>
-         <xs:enumeration value="xsd:gDay"/>
-         <xs:enumeration value="xsd:gMonth"/>
-         <xs:enumeration value="xsd:hexBinary"/>
-         <xs:enumeration value="xsd:base64Binary"/>
-         <xs:enumeration value="xsd:anyURI"/>
-         <xs:enumeration value="xsd:normalizedString"/>
-         <xs:enumeration value="xsd:token"/>
-         <xs:enumeration value="xsd:integer"/>
-         <xs:enumeration value="xsd:nonPositiveInteger"/>
-         <xs:enumeration value="xsd:negativeInteger"/>
-         <xs:enumeration value="xsd:long"/>
-         <xs:enumeration value="xsd:int"/>
-         <xs:enumeration value="xsd:short"/>
-         <xs:enumeration value="xsd:byte"/>
-         <xs:enumeration value="xsd:nonNegativeInteger"/>
-         <xs:enumeration value="xsd:unsignedLong"/>
-         <xs:enumeration value="xsd:unsignedInt"/>
-         <xs:enumeration value="xsd:unsignedShort"/>
-         <xs:enumeration value="xsd:unsignedByte"/>
-         <xs:enumeration value="xsd:positiveInteger"/>
-      </xs:restriction>
-   </xs:simpleType>
-   <!--Uri-->
-   <xs:complexType name="Uri">
-      <xs:annotation>
-         <xs:documentation> 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'). </xs:documentation>
-      </xs:annotation>
-      <xs:simpleContent>
-         <xs:extension base="xs:anyURI">
-            <xs:attribute name="desc" type="xs:token"/>
-            <xs:attribute name="type" type="xs:token"/>
-         </xs:extension>
-      </xs:simpleContent>
-   </xs:complexType>
-   <!-- Confidence:-->
-   <xs:complexType name="Confidence">
-      <xs:annotation>
-         <xs:documentation> 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').</xs:documentation>
-      </xs:annotation>
-      <xs:simpleContent>
-         <xs:extension base="xs:double">
-            <xs:attribute name="type" type="xs:token" use="required"/>
-         </xs:extension>
-      </xs:simpleContent>
-   </xs:complexType>
-   <!-- Identifier:-->
-   <xs:complexType name="Id">
-      <xs:annotation>
-         <xs:documentation> A general purpose identifier element. Allows to indicate the provider (or authority) of an
-            identifier. </xs:documentation>
-      </xs:annotation>
-      <xs:simpleContent>
-         <xs:extension base="xs:token">
-            <xs:attribute name="provider" type="xs:token"/>
-         </xs:extension>
-      </xs:simpleContent>
-   </xs:complexType>
-   <!-- Distribution:-->
-   <xs:complexType name="Distribution">
-      <xs:annotation>
-         <xs:documentation> The geographic distribution of the items of a clade (species, sequences), intended for
-            phylogeographic applications. The location can be described either by free text in the 'desc' element and/or
-            by the coordinates of one or more 'Points' (similar to the 'Point' element in Google's KML format) or by
-            'Polygons'. </xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="desc" type="xs:token" minOccurs="0"/>
-         <xs:element name="point" type="phy:Point" minOccurs="0" maxOccurs="unbounded"/>
-         <xs:element name="polygon" type="phy:Polygon" minOccurs="0" maxOccurs="unbounded"/>
-      </xs:sequence>
-   </xs:complexType>
-   <xs:complexType name="Point">
-      <xs:annotation>
-         <xs:documentation> The coordinates of a point with an optional altitude (used by element 'Distribution').
-            Required attributes are the 'geodetic_datum' used to indicate the geodetic datum (also called 'map datum',
-            for example Google's KML uses 'WGS84'). Attribute 'alt_unit' is the unit for the altitude (e.g. 'meter').
-         </xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="lat" type="xs:decimal"/>
-         <xs:element name="long" type="xs:decimal"/>
-         <xs:element name="alt" type="xs:decimal" minOccurs="0"/>
-      </xs:sequence>
-      <xs:attribute name="geodetic_datum" type="xs:token" use="required"/>
-      <xs:attribute name="alt_unit" type="xs:token"/>
-   </xs:complexType>
-   <xs:complexType name="Polygon">
-      <xs:annotation>
-         <xs:documentation> A polygon defined by a list of 'Points' (used by element 'Distribution').
-         </xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="point" type="phy:Point" minOccurs="3" maxOccurs="unbounded"/>
-      </xs:sequence>
-   </xs:complexType>
-   <!-- Date:-->
-   <xs:complexType name="Date">
-      <xs:annotation>
-         <xs:documentation> 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'). The elements 'minimum' and 'maximum' are used the indicate a range/confidence
-         interval</xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="desc" type="xs:token" minOccurs="0"/>
-         <xs:element name="value" type="xs:decimal" minOccurs="0"/>
-         <xs:element name="minimum" type="xs:decimal" minOccurs="0"/>
-         <xs:element name="maximum" type="xs:decimal" minOccurs="0"/>
-      </xs:sequence>
-      <xs:attribute name="unit" type="xs:token"/>
-   </xs:complexType>
-   <!-- BranchColor:-->
-   <xs:complexType name="BranchColor">
-      <xs:annotation>
-         <xs:documentation> This indicates the color of a clade when rendered (the color applies to the whole clade
-            unless overwritten by the color(s) of sub clades).</xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="red" type="xs:unsignedByte"/>
-         <xs:element name="green" type="xs:unsignedByte"/>
-         <xs:element name="blue" type="xs:unsignedByte"/>
-      </xs:sequence>
-   </xs:complexType>
-   <!-- SequenceRelation:-->
-   <xs:complexType name="SequenceRelation">
-      <xs:annotation>
-         <xs:documentation> 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'). </xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
-      </xs:sequence>
-      <xs:attribute name="id_ref_0" type="phy:id_ref" use="required"/>
-      <xs:attribute name="id_ref_1" type="phy:id_ref" use="required"/>
-      <xs:attribute name="distance" type="xs:double"/>
-      <xs:attribute name="type" type="phy:SequenceRelationType" use="required"/>
-   </xs:complexType>
-   <xs:simpleType name="SequenceRelationType">
-      <xs:restriction base="xs:token">
-         <xs:enumeration value="orthology"/>
-         <xs:enumeration value="one_to_one_orthology"/>
-         <xs:enumeration value="super_orthology"/>
-         <xs:enumeration value="paralogy"/>
-         <xs:enumeration value="ultra_paralogy"/>
-         <xs:enumeration value="xenology"/>
-         <xs:enumeration value="unknown"/>
-         <xs:enumeration value="other"/>
-      </xs:restriction>
-   </xs:simpleType>
-   <!-- CladeRelation:-->
-   <xs:complexType name="CladeRelation">
-      <xs:annotation>
-         <xs:documentation> This is used to express a typed relationship between two clades. For example it could be
-            used to describe multiple parents of a clade.</xs:documentation>
-      </xs:annotation>
-      <xs:sequence>
-         <xs:element name="confidence" type="phy:Confidence" minOccurs="0"/>
-      </xs:sequence>
-      <xs:attribute name="id_ref_0" type="phy:id_ref" use="required"/>
-      <xs:attribute name="id_ref_1" type="phy:id_ref" use="required"/>
-      <xs:attribute name="distance" type="xs:double"/>
-      <xs:attribute name="type" type="xs:token" use="required"/>
-   </xs:complexType>
-   <!-- Used to link elements together on the xml level:-->
-   <xs:simpleType name="id_source">
-      <xs:restriction base="xs:ID"/>
-   </xs:simpleType>
-   <xs:simpleType name="id_ref">
-      <xs:restriction base="xs:IDREF"/>
-   </xs:simpleType>
-</xs:schema>