<?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:include schemaLocation="../meta/sets.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 &lt;cell&gt; 
            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 StandardUncertainStateSet type is a single uncertain ambiguity mapping.
            </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 StandardPolymorphicStateSet type is a single polymorphic ambiguity mapping.                
            </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:element name="set" type="StateSet" 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:element name="set" minOccurs="0" maxOccurs="unbounded" type="CharSet"/>
                </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: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:element name="set" minOccurs="0" maxOccurs="unbounded" type="CellSet"/>
                </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:element name="set" minOccurs="0" maxOccurs="unbounded" type="RowSet"/>
                </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:element name="set" minOccurs="0" maxOccurs="unbounded" type="RowSet"/>
                </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>
