<?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 DNA character data. In a verbose notation, 
            this data is referenced by the "state" attribute of the &lt;cell&gt; 
            element, which points to a state element in the format block. I
            n 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="DNAToken">
        <xs:annotation>
            <xs:documentation>
                The DNAToken simple type is a restriction of AbstractSymbol that defines
                a token of a IUPAC single character nucleotide token.
            </xs:documentation>
        </xs:annotation>
        <xs:restriction base="AbstractSymbol">
            <xs:pattern value="[ABCDGHKMNRSTVWXY\-\?]"/>
            <xs:length value="1"/>
        </xs:restriction>
    </xs:simpleType>

    <xs:complexType name="DNAMapping">
        <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="DNAState">
        <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="DNAToken" use="required"/>
            </xs:restriction>
        </xs:complexContent>
    </xs:complexType>

    <xs:complexType name="DNAUncertainStateSet">
        <xs:annotation>
            <xs:documentation> 
                The DNAUncertainStateSet type defines an IUPAC ambiguity mapping. 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="DNAMapping" minOccurs="0" maxOccurs="unbounded"
                    />
                </xs:sequence>
                <xs:attribute name="symbol" type="DNAToken" use="required"/>
            </xs:restriction>
        </xs:complexContent>
    </xs:complexType>

    <xs:complexType name="DNAPolymorphicStateSet">
        <xs:annotation>
            <xs:documentation> 
                The DNAPolymorphicStateSet type defines an IUPAC ambiguity mapping. 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="DNAMapping" minOccurs="0" maxOccurs="unbounded"/>
                    <xs:element name="uncertain_state_set" type="DNAUncertainStateSet" minOccurs="0"
                        maxOccurs="unbounded"/>
                </xs:sequence>
                <xs:attribute name="symbol" type="DNAToken" use="required"/>
            </xs:restriction>
        </xs:complexContent>
    </xs:complexType>

    <xs:complexType name="DNAStates">
        <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="DNAState" minOccurs="0" maxOccurs="unbounded"/>
                    <xs:element name="polymorphic_state_set" type="DNAPolymorphicStateSet"
                        minOccurs="0" maxOccurs="unbounded"/>
                    <xs:element name="uncertain_state_set" type="DNAUncertainStateSet" 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="DNAChar"
        sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#NucleotideResidueCharacter">
        <xs:annotation>
            <xs:documentation> 
                A concrete implementation of the AbstractChar element.
            </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="optional"/>
                <xs:attribute name="id" type="xs:ID" use="required"/>
            </xs:restriction>
        </xs:complexContent>
    </xs:complexType>

    <xs:complexType name="DNAFormat" abstract="false">
        <xs:annotation>
            <xs:documentation> The DNAFormat class is the container of DNA column definitions.
            </xs:documentation>
        </xs:annotation>
        <xs:complexContent>
            <xs:restriction base="AbstractFormat">
                <xs:sequence minOccurs="1" maxOccurs="1">
                    <xs:element name="states" type="DNAStates" minOccurs="1" maxOccurs="unbounded"/>
                    <xs:element name="char" type="DNAChar" 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="DNAObs" abstract="false"
        sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#NucleotideStateDatum">
        <xs:annotation>
            <xs:documentation> 
                This is a single cell in a matrix containing a nucleotide 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="DNASeq">
        <xs:annotation>
            <xs:documentation> This is a simple type that specifies a sequence of DNA characters,
                following IUPAC single character symbols for nucleotides (and ambiguities).
            </xs:documentation>
        </xs:annotation>
        <xs:restriction base="AbstractSeq">
            <xs:pattern value="[\-\?ABCDGHKMNRSTVWXY\s]*"/>
        </xs:restriction>
    </xs:simpleType>

    <xs:complexType name="DNAMatrixSeqRow" abstract="false">
        <xs:annotation>
            <xs:documentation> This is a row in a matrix of DNA 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="DNASeq"/>
                </xs:sequence>
            </xs:restriction>
        </xs:complexContent>
    </xs:complexType>

    <xs:complexType name="DNAMatrixObsRow" abstract="false">
        <xs:annotation>
            <xs:documentation> This is a row in a matrix of DNA 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="DNAObs"/>
                    <xs:element name="set" minOccurs="0" maxOccurs="unbounded" type="CellSet"/>
                </xs:sequence>
            </xs:restriction>
        </xs:complexContent>
    </xs:complexType>

    <xs:complexType name="DNASeqMatrix" abstract="false">
        <xs:annotation>
            <xs:documentation>
                A matrix of rows with seq strings of type DNA.
            </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="DNAMatrixSeqRow"/>
                    <xs:element name="set" minOccurs="0" maxOccurs="unbounded" type="RowSet"/>
                </xs:sequence>
            </xs:restriction>
        </xs:complexContent>
    </xs:complexType>

    <xs:complexType name="DNAObsMatrix" 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="DNAMatrixObsRow"/>
                    <xs:element name="set" minOccurs="0" maxOccurs="unbounded" type="RowSet"/>
                </xs:sequence>
            </xs:restriction>
        </xs:complexContent>
    </xs:complexType>

    <xs:complexType name="DnaSeqs" abstract="false">
        <xs:annotation>
            <xs:documentation>
                A DNA 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="DNAFormat"/>
                    <xs:element name="matrix" minOccurs="1" maxOccurs="1" type="DNASeqMatrix"/>
                </xs:sequence>
            </xs:restriction>
        </xs:complexContent>
    </xs:complexType>

    <xs:complexType name="DnaCells" abstract="false">
        <xs:annotation>
            <xs:documentation>
                A DNA 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="DNAFormat"/>
                    <xs:element name="matrix" minOccurs="1" maxOccurs="1" type="DNAObsMatrix"/>
                </xs:sequence>
            </xs:restriction>
        </xs:complexContent>
    </xs:complexType>

</xs:schema>
