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 "standard" categorical character data, such as counts of morpholical features. In a verbose notation, this data is represented as the "state" attribute of the <cell> element. In a compact notation, the same data is represented as a sequence of space-separated integers.

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Complex types

StandardCells

Description

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

Inheritance

StandardCells restricts AbstractCells.

Substructures

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

Definition source

  <xs:complexType abstract="false" name="StandardCells">
    <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="StandardFormat"/>
          <xs:element maxOccurs="1" minOccurs="1" name="matrix" type="StandardObsMatrix"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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StandardChar

Description

A concrete implementation of the char element, which requires a states attribute to refer to a set of defined states

Inheritance

StandardChar restricts AbstractChar.

Attributes

Substructures

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

Definition source

  <xs:complexType name="StandardChar" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#StandardCharacter">
    <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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StandardFormat

Description

The StandardFormat class is the container of standard column definitions.

Inheritance

StandardFormat restricts AbstractFormat.

Substructures

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

Definition source

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

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StandardMapping

Description

A standard character ambiguity mapping.

Inheritance

StandardMapping restricts AbstractMapping.

Definition source

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

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StandardMatrixObsRow

Description

This is a row in a matrix of standard data as granular obervations.

Inheritance

StandardMatrixObsRow restricts AbstractObsRow.

Substructures

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

Definition source

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

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StandardMatrixSeqRow

Description

This is a row in a matrix of standard data as character sequences.

Inheritance

StandardMatrixSeqRow restricts AbstractSeqRow.

Substructures

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

Definition source

  <xs:complexType abstract="false" name="StandardMatrixSeqRow">
    <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="StandardSeq"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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StandardObs

Description

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

Inheritance

StandardObs restricts AbstractObs.

Attributes

Substructures

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

Definition source

  <xs:complexType abstract="false" name="StandardObs" sawsdl:modelReference="http://evolutionaryontology-dev.nescent.org/cdao.owl#StandardStateDatum">
    <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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StandardObsMatrix

Description

A matrix of rows with single character observations.

Inheritance

StandardObsMatrix restricts AbstractObsMatrix.

Substructures

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

Definition source

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

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StandardPolymorphicStateSet

Description

The StandardPolymorphicStateSet type is a single polymorphic ambiguity mapping.

Inheritance

StandardPolymorphicStateSet restricts AbstractPolymorphicStateSet.

Substructures

• an element called "member", instance of StandardMapping (0..unbounded).
• an element called "uncertain_state_set", instance of StandardUncertainStateSet (0..unbounded).

Definition source

  <xs:complexType name="StandardPolymorphicStateSet">
    <xs:complexContent>
      <xs:restriction base="AbstractPolymorphicStateSet">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="0" name="member" type="StandardMapping"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="uncertain_state_set" type="StandardUncertainStateSet"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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StandardSeqMatrix

Description

A matrix of rows with seq strings of type standard.

Inheritance

StandardSeqMatrix restricts AbstractSeqMatrix.

Substructures

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

Definition source

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

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StandardSeqs

Description

A standard characters block consisting of sequences preceded by metadata.

Inheritance

StandardSeqs restricts AbstractSeqs.

Substructures

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

Definition source

  <xs:complexType abstract="false" name="StandardSeqs">
    <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="StandardFormat"/>
          <xs:element maxOccurs="1" minOccurs="1" name="matrix" type="StandardSeqMatrix"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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StandardState

Description

This is a concrete implementation of the state element, which requires a symbol element, in this case restricted to integers, and optional mapping elements to refer to other states.

Inheritance

StandardState restricts AbstractState.

Attributes

Substructures

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

Definition source

  <xs:complexType name="StandardState">
    <xs:complexContent>
      <xs:restriction base="AbstractState">
        <xs:sequence maxOccurs="1" minOccurs="1">
          <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/>
        </xs:sequence>
        <xs:attribute name="symbol" type="StandardToken" use="required"/>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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StandardStates

Description

A container for a set of states.

Inheritance

StandardStates restricts AbstractStates.

Substructures

• an element called "meta", instance of Meta (0..unbounded).
• an element called "state", instance of StandardState (0..unbounded).
• an element called "polymorphic_state_set", instance of StandardPolymorphicStateSet (0..unbounded).
• an element called "uncertain_state_set", instance of StandardUncertainStateSet (0..unbounded).
• an element called "set", instance of StateSet (0..unbounded).

Definition source

  <xs:complexType name="StandardStates">
    <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="StandardState"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="polymorphic_state_set" type="StandardPolymorphicStateSet"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="uncertain_state_set" type="StandardUncertainStateSet"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="set" type="StateSet"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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StandardUncertainStateSet

Description

The StandardUncertainStateSet type is a single uncertain ambiguity mapping.

Inheritance

StandardUncertainStateSet restricts AbstractUncertainStateSet.

Attributes

Substructures

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

Definition source

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

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Simple types

StandardSeq

Description

This is a simple type that specifies a sequence of standard characters.

Inheritance

StandardSeq restricts AbstractTokenList.

Facets

Definition source

  <xs:simpleType name="StandardSeq">
    <xs:restriction base="AbstractTokenList">
      <xs:pattern value="[0-9\-\?]+(\s[0-9\-\?]+)*"/>
    </xs:restriction>
  </xs:simpleType>

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StandardToken

Inheritance

StandardToken restricts xs:integer.

Definition source

  <xs:simpleType name="StandardToken">
    <xs:restriction base="xs:integer"/>
  </xs:simpleType>

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See also

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

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

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

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

Quick links:

Libraries:

External links

• nexml@github
• NeXML wiki
• CDAO
• PhyloWS