<?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:xml="http://www.w3.org/XML/1998/namespace"
elementFormDefault="qualified">
<xs:include schemaLocation="abstractcharacters.xsd"/>

<!--
<xs:import namespace="http://www.w3.org/XML/1998/namespace"
    schemaLocation="http://www.w3.org/2001/xml.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 restriction site data. In a verbose notation, 
        this data is represented as the "state" attribute of the &lt;cell&gt; 
        element, whose value-space is limited to 0 or 1. In a compact 
        notation, the same data is represented as a sequence of tokens (whitespace is allowed but has no meaning).
    </xs:documentation>
</xs:annotation>     
<xs:simpleType name="RestrictionToken">
    <xs:restriction base="xs:integer">
        <xs:minInclusive value="0"/>
        <xs:maxInclusive value="1"/>
    </xs:restriction>
</xs:simpleType>

<!--
    A restriction site matrix only has presence (1) or absence (0), so
    state definitions and ambiguity mappings are omitted.

<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="RestrictionState">
    <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:attribute name="symbol" type="RestrictionToken" use="required"/>                
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

<xs:complexType name="RestrictionStates">
    <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="RestrictionState" minOccurs="2" maxOccurs="2"/>
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>        
</xs:complexType>

<xs:complexType name="RestrictionChar">
    <xs:annotation>
        <xs:documentation> 
            A concrete implementation of the char element, 
            which only requires a unique identifier.
        </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="RestrictionFormat" abstract="false">
    <xs:annotation>
        <xs:documentation> The RestrictionFormat class is the container of restriction column definitions.
        </xs:documentation>
    </xs:annotation>
    <xs:complexContent>
        <xs:restriction base="AbstractFormat">
            <xs:sequence minOccurs="1" maxOccurs="1">
                <xs:element name="states" type="RestrictionStates" minOccurs="1" maxOccurs="unbounded"/>
                <xs:element name="char" type="RestrictionChar" minOccurs="1" maxOccurs="unbounded"/>
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

<xs:complexType name="RestrictionObs" abstract="false">
    <xs:annotation>
        <xs:documentation> 
            This is a single cell in a matrix containing a 
            restriction site 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="RestrictionSeq">
    <xs:annotation>
        <xs:documentation> 
            This is a simple type that specifies a 
            sequence of restriction site characters.
        </xs:documentation>
    </xs:annotation>
    <xs:restriction base="xs:string">
        <xs:pattern value="[01\s]*"></xs:pattern>
    </xs:restriction>
</xs:simpleType>

<xs:complexType name="RestrictionMatrixSeqRow" abstract="false">
    <xs:annotation>
        <xs:documentation>
            This is a row in a matrix of restriction 
            site 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="RestrictionSeq"/>
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

<xs:complexType name="RestrictionMatrixObsRow" abstract="false">
    <xs:annotation>
        <xs:documentation> 
            This is a row in a matrix of restriction 
            site 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="RestrictionObs"/>
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

<xs:complexType name="RestrictionSeqMatrix" abstract="false">
    <xs:annotation>
        <xs:documentation>
            A matrix of rows with seq strings of type restriction.
        </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="RestrictionMatrixSeqRow"/>
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

<xs:complexType name="RestrictionObsMatrix" 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="RestrictionMatrixObsRow"/>
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

<xs:complexType name="RestrictionSeqs" abstract="false">
    <xs:annotation>
        <xs:documentation>
            A restriction site 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="RestrictionFormat"/>
                <xs:element name="matrix" minOccurs="1" maxOccurs="1" type="RestrictionSeqMatrix"/>
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

<xs:complexType name="RestrictionCells" 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="RestrictionFormat"/>
                <xs:element name="matrix" minOccurs="1" maxOccurs="1" type="RestrictionObsMatrix"/>                   
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

</xs:schema>