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 amino acid character data. In a verbose notation, this data is represented as the "state" attribute which references an explicitly defined state (either fundamental or ambiguous). In 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

AAChar

Description

A concrete implementation of the AbstractChar element.

Inheritance

AAChar restricts AbstractChar.

Attributes

Substructures

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

Definition source

  <xs:complexType name="AAChar" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#AminoAcidResidueCharacter">
    <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="prohibited"/>
        <xs:attribute name="id" type="xs:ID" use="required"/>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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AAFormat

Description

The AAFormat class is the container of amino acid column definitions.

Inheritance

AAFormat restricts AbstractFormat.

Substructures

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

Definition source

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

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AAMapping

Description

An IUPAC ambiguity mapping.

Inheritance

AAMapping restricts AbstractMapping.

Definition source

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

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AAMatrixObsRow

Description

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

Inheritance

AAMatrixObsRow restricts AbstractObsRow.

Substructures

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

Definition source

  <xs:complexType abstract="false" name="AAMatrixObsRow">
    <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="AAObs"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="set" type="CellSet"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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AAMatrixSeqRow

Description

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

Inheritance

AAMatrixSeqRow restricts AbstractSeqRow.

Substructures

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

Definition source

  <xs:complexType abstract="false" name="AAMatrixSeqRow">
    <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="AASeq"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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AAObs

Description

This is a single cell in a matrix containing an amino acid observation.

Inheritance

AAObs restricts AbstractObs.

Attributes

Substructures

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

Definition source

  <xs:complexType abstract="false" name="AAObs" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#AminoAcidResidueStateDatum">
    <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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AAObsMatrix

Description

A matrix of rows with single character observations.

Inheritance

AAObsMatrix restricts AbstractObsMatrix.

Substructures

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

Definition source

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

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AAPolymorphicStateSet

Description

The AAPolymorphicStateSet defines a polymorphic ambiguity mapping.

Inheritance

AAPolymorphicStateSet restricts AbstractPolymorphicStateSet.

Attributes

Substructures

• an element called "member", instance of AAMapping (0..unbounded).
• an element called "uncertain_state_set", instance of AAUncertainStateSet (0..unbounded).

Definition source

  <xs:complexType name="AAPolymorphicStateSet">
    <xs:complexContent>
      <xs:restriction base="AbstractPolymorphicStateSet">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="0" name="member" type="AAMapping"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="uncertain_state_set" type="AAUncertainStateSet"/>
        </xs:sequence>
        <xs:attribute name="symbol" type="AAToken" use="required"/>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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AASeqMatrix

Description

A matrix of rows with amino acid data as sequence strings.

Inheritance

AASeqMatrix restricts AbstractSeqMatrix.

Substructures

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

Definition source

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

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AAState

Description

This is a concrete implementation of the state element, which requires a symbol element, in this case restricted to AAToken, i.e. a single IUPAC amino acid symbol, and optional mapping elements to refer to other states.

Inheritance

AAState restricts AbstractState.

Attributes

Definition source

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

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AAStates

Description

A container for a set of states.

Inheritance

AAStates restricts AbstractStates.

Substructures

• an element called "meta", instance of Meta (0..unbounded).
• an element called "state", instance of AAState (0..unbounded).
• an element called "polymorphic_state_set", instance of AAPolymorphicStateSet (0..unbounded).
• an element called "uncertain_state_set", instance of AAUncertainStateSet (0..unbounded).
• an element called "set", instance of StateSet (0..unbounded).

Definition source

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

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AAUncertainStateSet

Description

The AAUncertainStateSet defines an uncertain ambiguity mapping.

Inheritance

AAUncertainStateSet restricts AbstractUncertainStateSet.

Attributes

Substructures

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

Definition source

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

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ProteinCells

Description

An amino acid characters block consisting of granular cells preceded by metadata.

Inheritance

ProteinCells restricts AbstractCells.

Substructures

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

Definition source

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

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ProteinSeqs

Description

An amino acid characters block consisting of sequences preceded by metadata.

Inheritance

ProteinSeqs restricts AbstractSeqs.

Substructures

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

Definition source

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

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Simple types

AASeq

Description

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

Inheritance

AASeq restricts AbstractSeq.

Facets

Definition source

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

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AAToken

Description

The AAToken simple type is a restriction of AbstractSymbol that defines an IUPAC single character amino acid symbol.

Inheritance

AAToken restricts AbstractSymbol.

Facets

Definition source

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

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See also

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

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

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

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

Quick links:

Libraries:

External links

• nexml@github
• NeXML wiki
• CDAO
• PhyloWS