<?xml version=“1.0” encoding=“UTF-8”?> <xs:schema
xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="http://www.nexml.org/2009" xmlns="http://www.nexml.org/2009" xmlns:sawsdl="http://www.w3.org/ns/sawsdl" xmlns:xml="http://www.w3.org/XML/1998/namespace" elementFormDefault="qualified"> <xs:include schemaLocation="abstractcharacters.xsd"/> <xs:annotation> <xs:documentation> This module defines concrete subclasses for the <a href="../abstract">abstract</a> character matrix components that all character matrices must implement. The subclasses defined here apply to "standard" categorical character data, such as counts of morpholical features. In a verbose notation, this data is represented as the "state" attribute of the <cell> element. In a compact notation, the same data is represented as a sequence of space-separated integers. </xs:documentation> </xs:annotation> <xs:simpleType name="StandardToken"> <xs:restriction base="xs:integer"/> </xs:simpleType> <xs:complexType name="StandardMapping"> <xs:annotation> <xs:documentation>A standard character ambiguity mapping.</xs:documentation> </xs:annotation> <xs:complexContent> <xs:restriction base="AbstractMapping"/> </xs:complexContent> </xs:complexType> <xs:complexType name="StandardState"> <xs:annotation> <xs:documentation> This is a concrete implementation of the state element, which requires a symbol element, in this case restricted to integers, and optional mapping elements to refer to other states. </xs:documentation> </xs:annotation> <xs:complexContent> <xs:restriction base="AbstractState"> <xs:sequence minOccurs="1" maxOccurs="1"> <xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/> </xs:sequence> <xs:attribute name="symbol" type="StandardToken" use="required"/> </xs:restriction> </xs:complexContent> </xs:complexType> <xs:complexType name="StandardUncertainStateSet"> <xs:annotation> <xs:documentation> The AbstractState type is the superclass for a state definition. The element encloses a required AbstractSymbol element that in restricted concrete subclasses must be of a sensible type such as a single IUPAC character. It may enclose zero or more AbstractMapping elements to resolve ambiguities. </xs:documentation> </xs:annotation> <xs:complexContent> <xs:restriction base="AbstractUncertainStateSet"> <xs:sequence minOccurs="1" maxOccurs="1"> <xs:element name="member" type="StandardMapping" minOccurs="0" maxOccurs="unbounded"/> </xs:sequence> <xs:attribute name="symbol" type="xs:string" use="required"/> </xs:restriction> </xs:complexContent> </xs:complexType> <xs:complexType name="StandardPolymorphicStateSet"> <xs:annotation> <xs:documentation> The AbstractState type is the superclass for a state definition. The element encloses a required AbstractSymbol element that in restricted concrete subclasses must be of a sensible type such as a single IUPAC character. It may enclose zero or more AbstractMapping elements to resolve ambiguities. </xs:documentation> </xs:annotation> <xs:complexContent> <xs:restriction base="AbstractPolymorphicStateSet"> <xs:sequence minOccurs="1" maxOccurs="1"> <xs:element name="member" type="StandardMapping" minOccurs="0" maxOccurs="unbounded"/> <xs:element name="uncertain_state_set" type="StandardUncertainStateSet" minOccurs="0" maxOccurs="unbounded"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType> <xs:complexType name="StandardStates"> <xs:annotation> <xs:documentation> A container for a set of states. </xs:documentation> </xs:annotation> <xs:complexContent> <xs:restriction base="AbstractStates"> <xs:sequence minOccurs="1" maxOccurs="1"> <xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/> <xs:element name="state" type="StandardState" minOccurs="0" maxOccurs="unbounded"/> <xs:element name="polymorphic_state_set" type="StandardPolymorphicStateSet" minOccurs="0" maxOccurs="unbounded"/> <xs:element name="uncertain_state_set" type="StandardUncertainStateSet" minOccurs="0" maxOccurs="unbounded"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType> <xs:complexType name="StandardChar" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#StandardCharacter"> <xs:annotation> <xs:documentation> A concrete implementation of the char element, which requires a states attribute to refer to a set of defined states </xs:documentation> </xs:annotation> <xs:complexContent> <xs:restriction base="AbstractChar"> <xs:sequence minOccurs="1" maxOccurs="1"> <xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/> </xs:sequence> <xs:attribute name="tokens" type="MSTokenLength" use="prohibited"/> <xs:attribute name="states" type="xs:IDREF" use="required"/> <xs:attribute name="codon" type="CodonPosition" use="prohibited"/> <xs:attribute name="id" type="xs:ID" use="required"/> </xs:restriction> </xs:complexContent> </xs:complexType> <xs:complexType name="StandardFormat" abstract="false"> <xs:annotation> <xs:documentation> The StandardFormat class is the container of standard column definitions. </xs:documentation> </xs:annotation> <xs:complexContent> <xs:restriction base="AbstractFormat"> <xs:sequence minOccurs="1" maxOccurs="1"> <xs:element name="states" type="StandardStates" minOccurs="1" maxOccurs="unbounded"/> <xs:element name="char" type="StandardChar" minOccurs="1" maxOccurs="unbounded"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType> <xs:complexType name="StandardObs" abstract="false" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#StandardStateDatum"> <xs:annotation> <xs:documentation> This is a single cell in a matrix containing a standard observation. </xs:documentation> </xs:annotation> <xs:complexContent> <xs:restriction base="AbstractObs"> <xs:sequence minOccurs="1" maxOccurs="1"> <xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/> </xs:sequence> <xs:attribute name="char" use="required" type="xs:IDREF"/> <xs:attribute name="state" use="required" type="xs:IDREF"/> </xs:restriction> </xs:complexContent> </xs:complexType> <xs:simpleType name="StandardSeq"> <xs:annotation> <xs:documentation> This is a simple type that specifies a sequence of standard characters. </xs:documentation> </xs:annotation> <xs:restriction base="AbstractTokenList"> <xs:pattern value="[0-9\-\?]+(\s[0-9\-\?]+)*"></xs:pattern> </xs:restriction> </xs:simpleType> <xs:complexType name="StandardMatrixSeqRow" abstract="false"> <xs:annotation> <xs:documentation> This is a row in a matrix of standard data as character sequences. </xs:documentation> </xs:annotation> <xs:complexContent> <xs:restriction base="AbstractSeqRow"> <xs:sequence minOccurs="1" maxOccurs="1"> <xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/> <xs:element name="seq" minOccurs="1" maxOccurs="1" type="StandardSeq"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType> <xs:complexType name="StandardMatrixObsRow" abstract="false"> <xs:annotation> <xs:documentation> This is a row in a matrix of standard data as granular obervations. </xs:documentation> </xs:annotation> <xs:complexContent> <xs:restriction base="AbstractObsRow"> <xs:sequence minOccurs="1" maxOccurs="1"> <xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/> <xs:element name="cell" minOccurs="1" maxOccurs="unbounded" type="StandardObs"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType> <xs:complexType name="StandardSeqMatrix" abstract="false"> <xs:annotation> <xs:documentation> A matrix of rows with seq strings of type standard. </xs:documentation> </xs:annotation> <xs:complexContent> <xs:restriction base="AbstractSeqMatrix"> <xs:sequence minOccurs="1" maxOccurs="1"> <xs:element name="row" minOccurs="1" maxOccurs="unbounded" type="StandardMatrixSeqRow"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType> <xs:complexType name="StandardObsMatrix" abstract="false"> <xs:annotation> <xs:documentation> A matrix of rows with single character observations. </xs:documentation> </xs:annotation> <xs:complexContent> <xs:restriction base="AbstractObsMatrix"> <xs:sequence minOccurs="1" maxOccurs="1"> <xs:element name="row" minOccurs="1" maxOccurs="unbounded" type="StandardMatrixObsRow"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType> <xs:complexType name="StandardSeqs" abstract="false"> <xs:annotation> <xs:documentation> A standard characters block consisting of sequences preceded by metadata. </xs:documentation> </xs:annotation> <xs:complexContent> <xs:restriction base="AbstractSeqs"> <xs:sequence minOccurs="1" maxOccurs="1"> <xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/> <xs:element name="format" minOccurs="1" maxOccurs="1" type="StandardFormat"/> <xs:element name="matrix" minOccurs="1" maxOccurs="1" type="StandardSeqMatrix"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType> <xs:complexType name="StandardCells" abstract="false"> <xs:annotation> <xs:documentation> A standard characters block consisting of granular cells preceded by metadata. </xs:documentation> </xs:annotation> <xs:complexContent> <xs:restriction base="AbstractCells"> <xs:sequence minOccurs="1" maxOccurs="1"> <xs:element name="meta" minOccurs="0" maxOccurs="unbounded" type="Meta"/> <xs:element name="format" minOccurs="1" maxOccurs="1" type="StandardFormat"/> <xs:element name="matrix" minOccurs="1" maxOccurs="1" type="StandardObsMatrix"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType>
</xs:schema>