[nexml]
phylogenetic data in xmlThe 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
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| 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 "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 "dict", instance of Dict (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="dict" type="Dict"/> <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
| Name | Type | Usage |
| tokens | MSTokenLength | prohibited |
| states | xs:NCName | required |
| codon | CodonPosition | prohibited |
| id | xs:NCName | required |
Substructures
- an element called "dict", instance of Dict (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="dict" type="Dict"/> </xs:sequence> <xs:attribute name="tokens" type="MSTokenLength" use="prohibited"/> <xs:attribute name="states" type="xs:NCName" use="required"/> <xs:attribute name="codon" type="CodonPosition" use="prohibited"/> <xs:attribute name="id" type="xs:NCName" 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).
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: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 "dict", instance of Dict (0..unbounded).
- an element called "cell", instance of StandardObs (1..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="dict" type="Dict"/> <xs:element maxOccurs="unbounded" minOccurs="1" name="cell" type="StandardObs"/> </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 "dict", instance of Dict (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="dict" type="Dict"/> <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
| Name | Type | Usage |
| char | xs:NCName | required |
| state | xs:NCName | required |
Substructures
- an element called "dict", instance of Dict (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="dict" type="Dict"/> </xs:sequence> <xs:attribute name="char" type="xs:NCName" use="required"/> <xs:attribute name="state" type="xs:NCName" 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).
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:sequence> </xs:restriction> </xs:complexContent> </xs:complexType>
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StandardPolymorphicStateSet
Description
The AbstractState type is the superclass for a state definition. The element encloses a required AbstractSymbol element that in restricted concrete subclasses must be of a sensible type such as a single IUPAC character. It may enclose zero or more AbstractMapping elements to resolve ambiguities.
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).
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: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 "dict", instance of Dict (0..unbounded).
- an element called "format", instance of StandardFormat (0..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="dict" type="Dict"/> <xs:element maxOccurs="1" minOccurs="0" 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
| Name | Type | Usage |
| symbol | StandardToken | required |
Substructures
- an element called "dict", instance of Dict (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="dict" type="Dict"/> </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 "dict", instance of Dict (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).
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="dict" type="Dict"/> <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:sequence> </xs:restriction> </xs:complexContent> </xs:complexType>
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StandardUncertainStateSet
Description
The AbstractState type is the superclass for a state definition. The element encloses a required AbstractSymbol element that in restricted concrete subclasses must be of a sensible type such as a single IUPAC character. It may enclose zero or more AbstractMapping elements to resolve ambiguities.
Inheritance
StandardUncertainStateSet restricts AbstractUncertainStateSet.
Attributes
| Name | Type | Usage |
| symbol | xs:string | required |
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
| Type | Value |
| pattern | [0-9]+(\s[0-9]+)* |
Definition source
<xs:simpleType name="StandardSeq"> <xs:restriction base="AbstractTokenList"> <xs:pattern value="[0-9]+(\s[0-9]+)*"></xs:pattern> </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/standard.xsd is included in:
This page summarizes the contents of schema file "~/nexml/xsd/characters/standard.xsd" as of revision 654. That schema file was last modified by rvos on 2008-09-22 15:17:49 -0400 (Mon, 22 Sep 2008), and this HTML summary page was generated on Tue Dec 16 16:26:28 2008.