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phylogenetic data in xml

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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 / dna

| Tue Dec 16 16:26:28 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 DNA character data. In a verbose notation, this data is represented as the "state" attribute of the <cell> element, whose value-space is limited to the IUPAC single character nucleotide symbols (except U). 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

DNAChar

Description

A concrete implementation of the AbstractChar element. In this implementation there is no reference to explicitly defined states, as we use the IUPAC standard. There may be a CodonPosition ("codon") attribute, and there must be an identifier ("id") that is of type xs:nonNegativeInteger to define the column number.

Inheritance

DNAChar restricts AbstractChar.

Attributes

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

Substructures

an element called "dict", instance of Dict (0..unbounded).

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="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="optional"/>
        <xs:attribute name="id" type="xs:NCName" use="required"/>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DNAFormat

Description

The DNAFormat class is the container of DNA column definitions.

Inheritance

DNAFormat restricts AbstractFormat.

Substructures

an element called "char", instance of DNAChar (1..unbounded).

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="char" type="DNAChar"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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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>

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DNAMatrixObsRow

Description

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

Inheritance

DNAMatrixObsRow restricts AbstractObsRow.

Substructures

an element called "dict", instance of Dict (0..unbounded).
an element called "cell", instance of DNAObs (1..unbounded).

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="dict" type="Dict"/>
          <xs:element maxOccurs="unbounded" minOccurs="1" name="cell" type="DNAObs"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DNAMatrixSeqRow

Description

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

Inheritance

DNAMatrixSeqRow restricts AbstractSeqRow.

Substructures

an element called "dict", instance of Dict (0..unbounded).
an element called "seq", instance of DNASeq (1..1).

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="dict" type="Dict"/>
          <xs:element maxOccurs="1" minOccurs="1" name="seq" type="DNASeq"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DNAObs

Description

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

Inheritance

DNAObs restricts AbstractObs.

Attributes

Name	Type	Usage
char	xs:nonNegativeInteger	required
state	DNAToken	required

Substructures

an element called "dict", instance of Dict (0..unbounded).

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="dict" type="Dict"/>
        </xs:sequence>
        <xs:attribute name="char" type="xs:nonNegativeInteger" use="required"/>
        <xs:attribute name="state" type="DNAToken" use="required"/>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DNAObsMatrix

Description

A matrix of rows with single character observations.

Inheritance

DNAObsMatrix restricts AbstractObsMatrix.

Substructures

an element called "row", instance of DNAMatrixObsRow (1..unbounded).

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

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DNASeqMatrix

Description

A matrix of rows with seq strings of type DNA.

Inheritance

DNASeqMatrix restricts AbstractSeqMatrix.

Substructures

an element called "row", instance of DNAMatrixSeqRow (1..unbounded).

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

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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.

Definition source

  <xs:complexType name="DNAState">
    <xs:complexContent>
      <xs:restriction base="AbstractState">
        <xs:sequence maxOccurs="1" minOccurs="1"/>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DNAStates

Description

A container for a set of states.

Inheritance

DNAStates restricts AbstractStates.

Substructures

an element called "dict", instance of Dict (0..unbounded).
an element called "state", instance of DNAState (0..unbounded).

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="dict" type="Dict"/>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="state" type="DNAState"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DnaCells

Description

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

Inheritance

DnaCells restricts AbstractCells.

Substructures

an element called "dict", instance of Dict (0..unbounded).
an element called "format", instance of DNAFormat (0..1).
an element called "matrix", instance of DNAObsMatrix (1..1).

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="dict" type="Dict"/>
          <xs:element maxOccurs="1" minOccurs="0" name="format" type="DNAFormat"/>
          <xs:element maxOccurs="1" minOccurs="1" name="matrix" type="DNAObsMatrix"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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DnaSeqs

Description

A DNA characters block consisting of sequences preceded by metadata.

Inheritance

DnaSeqs restricts AbstractSeqs.

Substructures

an element called "dict", instance of Dict (0..unbounded).
an element called "format", instance of DNAFormat (0..1).
an element called "matrix", instance of DNASeqMatrix (1..1).

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="dict" type="Dict"/>
          <xs:element maxOccurs="1" minOccurs="0" name="format" type="DNAFormat"/>
          <xs:element maxOccurs="1" minOccurs="1" name="matrix" type="DNASeqMatrix"/>
        </xs:sequence>
      </xs:restriction>
    </xs:complexContent>
  </xs:complexType>

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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>

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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>

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nexml schema 1.0 ~/nexml/xsd/characters/dna.xsd

[nexml]

The future data exchange standard is here!

Schema module documentation

Description

Complex types

DNAChar

Description

Inheritance

Attributes

Substructures

Definition source

DNAFormat

Description

Inheritance

Substructures

Definition source

DNAMapping

Description

Inheritance

Definition source

DNAMatrixObsRow

Description

Inheritance

Substructures

Definition source

DNAMatrixSeqRow

Description

Inheritance

Substructures

Definition source

DNAObs

Description

Inheritance

Attributes

Substructures

Definition source

DNAObsMatrix

Description

Inheritance

Substructures

Definition source

DNASeqMatrix

Description

Inheritance

Substructures

Definition source

DNAState

Description

Inheritance

Definition source

DNAStates

Description

Inheritance

Substructures

Definition source

DnaCells

Description

Inheritance

Substructures

Definition source

DnaSeqs

Description

Inheritance

Substructures

Definition source

Simple types

DNASeq

Description

Inheritance

Facets

Definition source

DNAToken

Description

Inheritance

Facets

Definition source

See also

Quick links:

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