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Schema module documentation

~ / doc / schema-1 / characters / restriction

— 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 restriction site data. In a verbose notation, this data is represented as the "state" attribute which references an explicit state definition. 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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schema source

Complex types

RestrictionCells

Description

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

Inheritance

RestrictionCells restricts AbstractCells.

Substructures

an element called "meta", instance of Meta (0..unbounded).
an element called "format", instance of RestrictionFormat (1..1).
an element called "matrix", instance of RestrictionObsMatrix (1..1).

Definition source

  <xs:complexType abstract="false" name="RestrictionCells">
    <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="RestrictionFormat"/>
          <xs:element maxOccurs="1" minOccurs="1" name="matrix" type="RestrictionObsMatrix"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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RestrictionChar

Description

A concrete implementation of the char element, which requires a unique identifier and a state set reference.

Inheritance

RestrictionChar restricts AbstractChar.

Attributes

Name	Type	Usage
tokens	MSTokenLength	prohibited
states	xs:IDREF	required
codon	CodonPosition	prohibited
id	xs:ID	required

Substructures

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

Definition source

  <xs:complexType name="RestrictionChar">
    <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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RestrictionFormat

Description

The RestrictionFormat class is the container of restriction column definitions.

Inheritance

RestrictionFormat restricts AbstractFormat.

Substructures

an element called "states", instance of RestrictionStates (1..unbounded).
an element called "char", instance of RestrictionChar (1..unbounded).
an element called "set", instance of CharSet (0..unbounded).

Definition source

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

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RestrictionMatrixObsRow

Description

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

Inheritance

RestrictionMatrixObsRow restricts AbstractObsRow.

Substructures

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

Definition source

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

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RestrictionMatrixSeqRow

Description

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

Inheritance

RestrictionMatrixSeqRow restricts AbstractSeqRow.

Substructures

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

Definition source

  <xs:complexType abstract="false" name="RestrictionMatrixSeqRow">
    <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="RestrictionSeq"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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RestrictionObs

Description

This is a single cell in a matrix containing a restriction site observation.

Inheritance

RestrictionObs restricts AbstractObs.

Attributes

Name	Type	Usage
char	xs:IDREF	required
state	xs:IDREF	required

Substructures

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

Definition source

  <xs:complexType abstract="false" name="RestrictionObs">
    <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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RestrictionObsMatrix

Description

A matrix of rows with single character observations.

Inheritance

RestrictionObsMatrix restricts AbstractObsMatrix.

Substructures

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

Definition source

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

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RestrictionSeqMatrix

Description

A matrix of rows with seq strings of type restriction.

Inheritance

RestrictionSeqMatrix restricts AbstractSeqMatrix.

Substructures

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

Definition source

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

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RestrictionSeqs

Description

A restriction site characters block consisting of sequences preceded by metadata.

Inheritance

RestrictionSeqs restricts AbstractSeqs.

Substructures

an element called "meta", instance of Meta (0..unbounded).
an element called "format", instance of RestrictionFormat (1..1).
an element called "matrix", instance of RestrictionSeqMatrix (1..1).

Definition source

  <xs:complexType abstract="false" name="RestrictionSeqs">
    <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="RestrictionFormat"/>
          <xs:element maxOccurs="1" minOccurs="1" name="matrix" type="RestrictionSeqMatrix"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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RestrictionState

Description

This is a concrete implementation of the state element, which requires a symbol element, in this case restricted to 0/1.

Inheritance

RestrictionState restricts AbstractState.

Attributes

Name	Type	Usage
symbol	RestrictionToken	required

Definition source

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

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RestrictionStates

Description

A container for a set of states.

Inheritance

RestrictionStates restricts AbstractStates.

Substructures

an element called "meta", instance of Meta (0..unbounded).
an element called "state", instance of RestrictionState (2..2).
an element called "set", instance of StateSet (0..unbounded).

Definition source

  <xs:complexType name="RestrictionStates">
    <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="2" minOccurs="2" name="state" type="RestrictionState"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="set" type="StateSet"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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Simple types

RestrictionSeq

Description

This is a simple type that specifies a sequence of restriction site characters.

Inheritance

RestrictionSeq restricts xs:string.

Facets

Type	Value
pattern	[01\s]*

Definition source

  <xs:simpleType name="RestrictionSeq">
    <xs:restriction base="xs:string">
      <xs:pattern value="[01\s]*"/>
    </xs:restriction>
  </xs:simpleType>

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RestrictionToken

Inheritance

RestrictionToken restricts xs:integer.

Facets

Type	Value
minInclusive	0
maxInclusive	1

Definition source

  <xs:simpleType name="RestrictionToken">
    <xs:restriction base="xs:integer">
      <xs:minInclusive value="0"/>
      <xs:maxInclusive value="1"/>
    </xs:restriction>
  </xs:simpleType>

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

[NeXML]

The future data exchange standard is here!

Schema module documentation

Description

Complex types

RestrictionCells

Description

Inheritance

Substructures

Definition source

RestrictionChar

Description

Inheritance

Attributes

Substructures

Definition source

RestrictionFormat

Description

Inheritance

Substructures

Definition source

RestrictionMatrixObsRow

Description

Inheritance

Substructures

Definition source

RestrictionMatrixSeqRow

Description

Inheritance

Substructures

Definition source

RestrictionObs

Description

Inheritance

Attributes

Substructures

Definition source

RestrictionObsMatrix

Description

Inheritance

Substructures

Definition source

RestrictionSeqMatrix

Description

Inheritance

Substructures

Definition source

RestrictionSeqs

Description

Inheritance

Substructures

Definition source

RestrictionState

Description

Inheritance

Attributes

Definition source

RestrictionStates

Description

Inheritance

Substructures

Definition source

Simple types

RestrictionSeq

Description

Inheritance

Facets

Definition source

RestrictionToken

Inheritance

Facets

Definition source

See also

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External links