Schema module documentation

| — Last updated: Tue Sep 23 12:49:28 IST 2014

Description

This module defines concrete subclasses for the abstract 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 <cell> 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).

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Complex types

DNAChar

Description

A concrete implementation of the AbstractChar element.

Inheritance

DNAChar restricts AbstractChar.

Attributes

Substructures

• an element called "meta", instance of Meta (0..unbounded).

Definition source

  <xs:complexType name="DNAChar" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#NucleotideResidueCharacter">
    <xs:complexContent>
      <xs:restriction base="AbstractChar">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" 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>

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DNAFormat

Description

The DNAFormat class is the container of DNA column definitions.

Inheritance

DNAFormat restricts AbstractFormat.

Substructures

• an element called "states", instance of DNAStates (1..unbounded).
• an element called "char", instance of DNAChar (1..unbounded).
• an element called "set", instance of CharSet (0..unbounded).

Definition source

  <xs:complexType abstract="false" name="DNAFormat">
    <xs:complexContent>
      <xs:restriction base="AbstractFormat">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="1" name="states" type="DNAStates"/>
          <xs:element maxOccurs="unbounded" minOccurs="1" name="char" type="DNAChar"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="set" type="CharSet"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DNAMapping

Description

An IUPAC ambiguity mapping.

Inheritance

DNAMapping restricts AbstractMapping.

Definition source

  <xs:complexType name="DNAMapping">
    <xs:complexContent>
      <xs:restriction base="AbstractMapping"/>
    </xs:complexContent>
  </xs:complexType>

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DNAMatrixObsRow

Description

This is a row in a matrix of DNA data containing granular observations.

Inheritance

DNAMatrixObsRow restricts AbstractObsRow.

Substructures

• an element called "meta", instance of Meta (0..unbounded).
• an element called "cell", instance of DNAObs (1..unbounded).
• an element called "set", instance of CellSet (0..unbounded).

Definition source

  <xs:complexType abstract="false" name="DNAMatrixObsRow">
    <xs:complexContent>
      <xs:restriction base="AbstractObsRow">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/>
          <xs:element maxOccurs="unbounded" minOccurs="1" name="cell" type="DNAObs"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="set" type="CellSet"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DNAMatrixSeqRow

Description

This is a row in a matrix of DNA data containing raw sequence data.

Inheritance

DNAMatrixSeqRow restricts AbstractSeqRow.

Substructures

• an element called "meta", instance of Meta (0..unbounded).
• an element called "seq", instance of DNASeq (1..1).

Definition source

  <xs:complexType abstract="false" name="DNAMatrixSeqRow">
    <xs:complexContent>
      <xs:restriction base="AbstractSeqRow">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/>
          <xs:element maxOccurs="1" minOccurs="1" name="seq" type="DNASeq"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DNAObs

Description

This is a single cell in a matrix containing a nucleotide observation.

Inheritance

DNAObs restricts AbstractObs.

Attributes

Substructures

• an element called "meta", instance of Meta (0..unbounded).

Definition source

  <xs:complexType abstract="false" name="DNAObs" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#NucleotideStateDatum">
    <xs:complexContent>
      <xs:restriction base="AbstractObs">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/>
        </xs:sequence>
        <xs:attribute name="char" type="xs:IDREF" use="required"/>
        <xs:attribute name="state" type="xs:IDREF" use="required"/>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DNAObsMatrix

Description

A matrix of rows with single character observations.

Inheritance

DNAObsMatrix restricts AbstractObsMatrix.

Substructures

• an element called "row", instance of DNAMatrixObsRow (1..unbounded).
• an element called "set", instance of RowSet (0..unbounded).

Definition source

  <xs:complexType abstract="false" name="DNAObsMatrix">
    <xs:complexContent>
      <xs:restriction base="AbstractObsMatrix">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="1" name="row" type="DNAMatrixObsRow"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="set" type="RowSet"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DNAPolymorphicStateSet

Description

The DNAPolymorphicStateSet type defines an IUPAC ambiguity mapping. It may enclose zero or more AbstractMapping elements to resolve ambiguities.

Inheritance

DNAPolymorphicStateSet restricts AbstractPolymorphicStateSet.

Attributes

Substructures

• an element called "member", instance of DNAMapping (0..unbounded).
• an element called "uncertain_state_set", instance of DNAUncertainStateSet (0..unbounded).

Definition source

  <xs:complexType name="DNAPolymorphicStateSet">
    <xs:complexContent>
      <xs:restriction base="AbstractPolymorphicStateSet">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="0" name="member" type="DNAMapping"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="uncertain_state_set" type="DNAUncertainStateSet"/>
        </xs:sequence>
        <xs:attribute name="symbol" type="DNAToken" use="required"/>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DNASeqMatrix

Description

A matrix of rows with seq strings of type DNA.

Inheritance

DNASeqMatrix restricts AbstractSeqMatrix.

Substructures

• an element called "row", instance of DNAMatrixSeqRow (1..unbounded).
• an element called "set", instance of RowSet (0..unbounded).

Definition source

  <xs:complexType abstract="false" name="DNASeqMatrix">
    <xs:complexContent>
      <xs:restriction base="AbstractSeqMatrix">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="1" name="row" type="DNAMatrixSeqRow"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="set" type="RowSet"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DNAState

Description

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.

Inheritance

DNAState restricts AbstractState.

Attributes

Definition source

  <xs:complexType name="DNAState">
    <xs:complexContent>
      <xs:restriction base="AbstractState">
        <xs:sequence maxOccurs="1" minOccurs="1"/>
        <xs:attribute name="symbol" type="DNAToken" use="required"/>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DNAStates

Description

A container for a set of states.

Inheritance

DNAStates restricts AbstractStates.

Substructures

• an element called "meta", instance of Meta (0..unbounded).
• an element called "state", instance of DNAState (0..unbounded).
• an element called "polymorphic_state_set", instance of DNAPolymorphicStateSet (0..unbounded).
• an element called "uncertain_state_set", instance of DNAUncertainStateSet (0..unbounded).
• an element called "set", instance of StateSet (0..unbounded).

Definition source

  <xs:complexType name="DNAStates">
    <xs:complexContent>
      <xs:restriction base="AbstractStates">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="state" type="DNAState"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="polymorphic_state_set" type="DNAPolymorphicStateSet"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="uncertain_state_set" type="DNAUncertainStateSet"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="set" type="StateSet"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DNAUncertainStateSet

Description

The DNAUncertainStateSet type defines an IUPAC ambiguity mapping. It may enclose zero or more AbstractMapping elements to resolve ambiguities.

Inheritance

DNAUncertainStateSet restricts AbstractUncertainStateSet.

Attributes

Substructures

• an element called "member", instance of DNAMapping (0..unbounded).

Definition source

  <xs:complexType name="DNAUncertainStateSet">
    <xs:complexContent>
      <xs:restriction base="AbstractUncertainStateSet">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="0" name="member" type="DNAMapping"/>
        </xs:sequence>
        <xs:attribute name="symbol" type="DNAToken" use="required"/>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DnaCells

Description

A DNA characters block consisting of granular cells preceded by metadata.

Inheritance

DnaCells restricts AbstractCells.

Substructures

• an element called "meta", instance of Meta (0..unbounded).
• an element called "format", instance of DNAFormat (1..1).
• an element called "matrix", instance of DNAObsMatrix (1..1).

Definition source

  <xs:complexType abstract="false" name="DnaCells">
    <xs:complexContent>
      <xs:restriction base="AbstractCells">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/>
          <xs:element maxOccurs="1" minOccurs="1" name="format" type="DNAFormat"/>
          <xs:element maxOccurs="1" minOccurs="1" name="matrix" type="DNAObsMatrix"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DnaSeqs

Description

A DNA characters block consisting of sequences preceded by metadata.

Inheritance

DnaSeqs restricts AbstractSeqs.

Substructures

• an element called "meta", instance of Meta (0..unbounded).
• an element called "format", instance of DNAFormat (1..1).
• an element called "matrix", instance of DNASeqMatrix (1..1).

Definition source

  <xs:complexType abstract="false" name="DnaSeqs">
    <xs:complexContent>
      <xs:restriction base="AbstractSeqs">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/>
          <xs:element maxOccurs="1" minOccurs="1" name="format" type="DNAFormat"/>
          <xs:element maxOccurs="1" minOccurs="1" name="matrix" type="DNASeqMatrix"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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Simple types

DNASeq

Description

This is a simple type that specifies a sequence of DNA characters, following IUPAC single character symbols for nucleotides (and ambiguities).

Inheritance

DNASeq restricts AbstractSeq.

Facets

Definition source

  <xs:simpleType name="DNASeq">
    <xs:restriction base="AbstractSeq">
      <xs:pattern value="[\-\?ABCDGHKMNRSTVWXY\s]*"/>
    </xs:restriction>
  </xs:simpleType>

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DNAToken

Description

The DNAToken simple type is a restriction of AbstractSymbol that defines a token of a IUPAC single character nucleotide token.

Inheritance

DNAToken restricts AbstractSymbol.

Facets

Definition source

  <xs:simpleType name="DNAToken">
    <xs:restriction base="AbstractSymbol">
      <xs:pattern value="[ABCDGHKMNRSTVWXY\-\?]"/>
      <xs:length value="1"/>
    </xs:restriction>
  </xs:simpleType>

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See also

~/nexml/xsd/characters/dna.xsd includes the following other files:

• ~/nexml/xsd/characters/abstractcharacters.xsd
• ~/nexml/xsd/meta/sets.xsd

~/nexml/xsd/characters/dna.xsd is included in:

• ~/nexml/xsd/characters/characters.xsd

Quick links:

Libraries:

External links

• nexml@github
• NeXML wiki
• CDAO
• PhyloWS