nexml schema 0.9 ~/nexml/xsd/characters/dna.xsd

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Schema module documentation

~ / doc / schema-1 / characters / dna
rss | digg reddit del.icio.us facebook — 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
Name Type Usage
tokens MSTokenLength prohibited
states xs:IDREF required
codon CodonPosition optional
id xs:ID required
Substructures
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>

DNAFormat

Description

The DNAFormat class is the container of DNA column definitions.

Inheritance

DNAFormat restricts AbstractFormat.

Substructures
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>

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>

DNAMatrixObsRow

Description

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

Inheritance

DNAMatrixObsRow restricts AbstractObsRow.

Substructures
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>

DNAMatrixSeqRow

Description

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

Inheritance

DNAMatrixSeqRow restricts AbstractSeqRow.

Substructures
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>

DNAObs

Description

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

Inheritance

DNAObs restricts AbstractObs.

Attributes
Name Type Usage
char xs:IDREF required
state xs:IDREF required
Substructures
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>

DNAObsMatrix

Description

A matrix of rows with single character observations.

Inheritance

DNAObsMatrix restricts AbstractObsMatrix.

Substructures
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>

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
Name Type Usage
symbol DNAToken required
Substructures
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>

DNASeqMatrix

Description

A matrix of rows with seq strings of type DNA.

Inheritance

DNASeqMatrix restricts AbstractSeqMatrix.

Substructures
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>

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
Name Type Usage
symbol DNAToken required
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>

DNAStates

Description

A container for a set of states.

Inheritance

DNAStates restricts AbstractStates.

Substructures
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>

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
Name Type Usage
symbol DNAToken required
Substructures
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>

DnaCells

Description

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

Inheritance

DnaCells restricts AbstractCells.

Substructures
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>

DnaSeqs

Description

A DNA characters block consisting of sequences preceded by metadata.

Inheritance

DnaSeqs restricts AbstractSeqs.

Substructures
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>

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

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

See also

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

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

This page summarizes the contents of schema file "~/nexml/xsd/characters/dna.xsd". Generated on Tue Sep 23 12:49:34 2014.