<?xml version=“1.0” encoding=“UTF-8”?> <xs:schema xmlns:xs=“www.w3.org/2001/XMLSchema

    targetNamespace="http://www.nexml.org/2009"
    xmlns:sawsdl="http://www.w3.org/ns/sawsdl"
xmlns="http://www.nexml.org/2009"
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 amino acid character 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 the IUPAC single character
        nucleotide symbols. 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="AAToken">
    <xs:annotation>
        <xs:documentation>
            The AAToken simple type is a restriction of AbstractSymbol 
            that defines an IUPAC single character amino acid symbol.
        </xs:documentation>
        <xs:appinfo>AminoAcid</xs:appinfo>
    </xs:annotation>
    <xs:restriction base="AbstractSymbol">
        <xs:pattern value="[\*\-\?ABCDEFGHIKLMNPQRSTUVWXYZ]"/>
        <xs:length value="1"/>
    </xs:restriction>
</xs:simpleType>

<xs:complexType name="AAChar" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#AminoAcidResidueCharacter">
    <xs:annotation>
        <xs:documentation> 
            A concrete implementation of the AbstractChar element. In this implementation
            there is no reference to explicitly defined states, as we use the IUPAC standard.
            There must be an identifier ("id") that is of type xs:nonNegativeInteger to 
            define the column number.
        </xs:documentation>
        <xs:appinfo>Amino_Acid_Character</xs:appinfo>
    </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="AAFormat" abstract="false">
    <xs:annotation>
        <xs:documentation> The AAFormat class is the container of amino acid column definitions.
        </xs:documentation>
    </xs:annotation>
    <xs:complexContent>
        <xs:restriction base="AbstractFormat">
            <xs:sequence minOccurs="1" maxOccurs="1">
                <xs:element name="states" type="AAStates" minOccurs="1" maxOccurs="unbounded"/>                
                <xs:element name="char" type="AAChar" minOccurs="1" maxOccurs="unbounded"/>
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

<xs:complexType name="AAStates">
    <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="AAState" minOccurs="0" maxOccurs="unbounded"/>
                <xs:element name="polymorphic_state_set" type="AAPolymorphicStateSet" minOccurs="0" maxOccurs="unbounded"/>
                <xs:element name="uncertain_state_set" type="AAUncertainStateSet" minOccurs="0" maxOccurs="unbounded"/>                    
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>        
</xs:complexType>   

<xs:complexType name="AAPolymorphicStateSet">
    <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="AAMapping" minOccurs="0" maxOccurs="unbounded"/>
                <xs:element name="uncertain_state_set" type="AAUncertainStateSet" minOccurs="0" maxOccurs="unbounded"/>
            </xs:sequence>
            <xs:attribute name="symbol" type="AAToken" use="required"></xs:attribute>                
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>   

<xs:complexType name="AAUncertainStateSet">
    <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="AAMapping" minOccurs="0" maxOccurs="unbounded"/>
            </xs:sequence>
            <xs:attribute name="symbol" type="AAToken" use="required"></xs:attribute>                
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>        

<xs:complexType name="AAMapping">
    <xs:annotation>
        <xs:documentation>An IUPAC ambiguity mapping.</xs:documentation>
    </xs:annotation>
    <xs:complexContent>
        <xs:restriction base="AbstractMapping"/>            
    </xs:complexContent>
</xs:complexType>    

<xs:complexType name="AAState">
    <xs:annotation>
        <xs:documentation> 
            This is a concrete implementation of the state element, which requires
            a symbol element, in this case restricted to DNAToken, i.e. a single IUPAC nucleotide
            symbol, 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="AAToken" use="required"></xs:attribute>                
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>     

<xs:complexType name="AAObs" abstract="false" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#AminoAcidResidueStateDatum">
    <xs:annotation>
        <xs:documentation> 
            This is a single cell in a matrix containing
            an amino acid observation. 
        </xs:documentation>
        <xs:appinfo>Amino_Acid_State_Datum</xs:appinfo>
    </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="AASeq">
    <xs:annotation>
        <xs:documentation> 
            This is a simple type that specifies a sequence of amino acid characters,
            following IUPAC single character symbols for aa (and ambiguities).
        </xs:documentation>
    </xs:annotation>
    <xs:restriction base="AbstractSeq">
        <xs:pattern value="[\*\-\?ABCDEFGHIKLMNPQRSTUVWXYZ\s]*"/>
    </xs:restriction>
</xs:simpleType>

<xs:complexType name="AAMatrixSeqRow" abstract="false">
    <xs:annotation>
        <xs:documentation> This is a row in a matrix of amino acid data containing raw sequence data. </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="AASeq"/>
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

<xs:complexType name="AAMatrixObsRow" abstract="false">
    <xs:annotation>
        <xs:documentation> This is a row in a matrix of amino acid data containing granular observations. </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="AAObs"/>
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

<xs:complexType name="AASeqMatrix" abstract="false">
    <xs:annotation>
        <xs:documentation>
            A matrix of rows with amino acid data as sequence strings.
        </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="AAMatrixSeqRow"/>
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

<xs:complexType name="AAObsMatrix" 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="AAMatrixObsRow"/>
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

<xs:complexType name="ProteinSeqs" abstract="false">
    <xs:annotation>
        <xs:documentation>
            An amino acid 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="AAFormat"/>
                <xs:element name="matrix" minOccurs="1" maxOccurs="1" type="AASeqMatrix"/>
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

<xs:complexType name="ProteinCells" abstract="false">
    <xs:annotation>
        <xs:documentation>
            An amino acid 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="AAFormat"/>
                <xs:element name="matrix" minOccurs="1" maxOccurs="1" type="AAObsMatrix"/>                   
            </xs:sequence>
        </xs:restriction>
    </xs:complexContent>
</xs:complexType>

</xs:schema>