[nexml]

phylogenetic data in xml

The future data exchange standard is here!

nexml is an exchange standard for representing phylogenetic data — inspired by the commonly used NEXUS format, but more robust and easier to process.

Schema module documentation

~ / nexml / html / doc / schema-1 / characters / restriction

| Mon Dec 1 18:56:49 2008 —

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 of the <cell> element, whose value-space is limited to 0 or 1. In a compact notation, the same data is represented as a sequence of tokens (whitespace is allowed but has no meaning).

Other views (open in new window):

inheritance tree |

inclusions tree |

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 "dict", instance of Dict (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="dict" type="Dict"/>
          <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>

[ Back to top ]

RestrictionChar

Description

A concrete implementation of the char element, which only requires a unique identifier.

Inheritance

RestrictionChar restricts AbstractChar.

Attributes

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

Substructures

an element called "dict", instance of Dict (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="dict" type="Dict"/>
        </xs:sequence>
        <xs:attribute name="tokens" type="MSTokenLength" use="prohibited"/>
        <xs:attribute name="states" type="xs:NCName" use="prohibited"/>
        <xs:attribute name="codon" type="CodonPosition" use="prohibited"/>
        <xs:attribute name="id" type="xs:NCName" use="required"/>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

[ Back to top ]

RestrictionFormat

Description

The RestrictionFormat class is the container of restriction column definitions.

Inheritance

RestrictionFormat restricts AbstractFormat.

Substructures

an element called "char", instance of RestrictionChar (1..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="char" type="RestrictionChar"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

[ Back to top ]

RestrictionMatrixObsRow

Description

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

Inheritance

RestrictionMatrixObsRow restricts AbstractObsRow.

Substructures

an element called "dict", instance of Dict (0..unbounded).
an element called "cell", instance of RestrictionObs (1..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="dict" type="Dict"/>
          <xs:element maxOccurs="unbounded" minOccurs="1" name="cell" type="RestrictionObs"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

[ Back to top ]

RestrictionMatrixSeqRow

Description

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

Inheritance

RestrictionMatrixSeqRow restricts AbstractSeqRow.

Substructures

an element called "dict", instance of Dict (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="dict" type="Dict"/>
          <xs:element maxOccurs="1" minOccurs="1" name="seq" type="RestrictionSeq"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

[ Back to top ]

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:nonNegativeInteger	required
state	RestrictionToken	required

Substructures

an element called "dict", instance of Dict (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="dict" type="Dict"/>
        </xs:sequence>
        <xs:attribute name="char" type="xs:nonNegativeInteger" use="required"/>
        <xs:attribute name="state" type="RestrictionToken" use="required"/>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

[ Back to top ]

RestrictionObsMatrix

Description

A matrix of rows with single character observations.

Inheritance

RestrictionObsMatrix restricts AbstractObsMatrix.

Substructures

an element called "row", instance of RestrictionMatrixObsRow (1..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:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

[ Back to top ]

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).

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:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

[ Back to top ]

RestrictionSeqs

Description

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

Inheritance

RestrictionSeqs restricts AbstractSeqs.

Substructures

an element called "dict", instance of Dict (0..unbounded).
an element called "format", instance of RestrictionFormat (0..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="dict" type="Dict"/>
          <xs:element maxOccurs="1" minOccurs="0" name="format" type="RestrictionFormat"/>
          <xs:element maxOccurs="1" minOccurs="1" name="matrix" type="RestrictionSeqMatrix"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

[ Back to top ]

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:pattern>
    </xs:restriction>
  </xs:simpleType>

[ Back to top ]

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>

[ Back to top ]

nexml schema 1.0 ~/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

Simple types

RestrictionSeq

Description

Inheritance

Facets

Definition source

RestrictionToken

Inheritance

Facets

Definition source

See also

Quick links:

Bindings:

Goings on:

External links