[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
|
| Tue Dec 16 16:26:29 2008 —
Description
This module defines the components of trees, graphs
where edges have an in-degree that of 1. The
types defined in this module are concrete implementations
that inherit from the abstract types in the
abstract trees module.
Depending on the concrete subclass, edges in trees either
have lengths formatted as integers or lengths formatted as
floating point numbers.
Other views (open in new window):
inheritance tree
inclusions tree
schema source
Complex types
FloatTree
Description
A concrete tree implementation, with floating point edge lengths.
Inheritance
FloatTree restricts AbstractTree.
Substructures
- an element called "node", instance of TreeNode (1..unbounded).
- an element called "rootedge", instance of TreeFloatRootEdge (0..1).
- an element called "edge", instance of TreeFloatEdge (1..unbounded).
Definition source
<xs:complexType abstract="false" name="FloatTree"> <xs:complexContent> <xs:restriction base="AbstractTree"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="1" name="node" type="TreeNode"/> <xs:element maxOccurs="1" minOccurs="0" name="rootedge" type="TreeFloatRootEdge"/> <xs:element maxOccurs="unbounded" minOccurs="1" name="edge" type="TreeFloatEdge"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType>
[ Back to top ]
IntTree
Description
A concrete tree implementation, with integer edge lengths.
Inheritance
IntTree restricts AbstractTree.
Substructures
- an element called "node", instance of TreeNode (1..unbounded).
- an element called "rootedge", instance of TreeIntRootEdge (0..1).
- an element called "edge", instance of TreeIntEdge (1..unbounded).
Definition source
<xs:complexType abstract="false" name="IntTree"> <xs:complexContent> <xs:restriction base="AbstractTree"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="1" name="node" type="TreeNode"/> <xs:element maxOccurs="1" minOccurs="0" name="rootedge" type="TreeIntRootEdge"/> <xs:element maxOccurs="unbounded" minOccurs="1" name="edge" type="TreeIntEdge"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType>
[ Back to top ]
TreeFloatEdge
Description
A concrete edge implementation, with float length.
Inheritance
TreeFloatEdge restricts AbstractEdge.
Attributes
| Name | Type | Usage |
| length | xs:float |
Substructures
- an element called "dict", instance of Dict (0..unbounded).
Definition source
<xs:complexType abstract="false" name="TreeFloatEdge"> <xs:complexContent> <xs:restriction base="AbstractEdge"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="0" name="dict" type="Dict"/> </xs:sequence> <xs:attribute name="length" type="xs:float"/> </xs:restriction> </xs:complexContent> </xs:complexType>
[ Back to top ]
TreeFloatRootEdge
Description
A concrete root edge implementation, with float length.
Inheritance
TreeFloatRootEdge restricts AbstractRootEdge.
Attributes
| Name | Type | Usage |
| length | xs:float |
Substructures
- an element called "dict", instance of Dict (0..unbounded).
Definition source
<xs:complexType abstract="false" name="TreeFloatRootEdge"> <xs:complexContent> <xs:restriction base="AbstractRootEdge"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="0" name="dict" type="Dict"/> </xs:sequence> <xs:attribute name="length" type="xs:float"/> </xs:restriction> </xs:complexContent> </xs:complexType>
[ Back to top ]
TreeIntEdge
Description
A concrete edge implementation, with int length.
Inheritance
TreeIntEdge restricts AbstractEdge.
Attributes
| Name | Type | Usage |
| length | xs:integer |
Substructures
- an element called "dict", instance of Dict (0..unbounded).
Definition source
<xs:complexType abstract="false" name="TreeIntEdge"> <xs:complexContent> <xs:restriction base="AbstractEdge"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="0" name="dict" type="Dict"/> </xs:sequence> <xs:attribute name="length" type="xs:integer"/> </xs:restriction> </xs:complexContent> </xs:complexType>
[ Back to top ]
TreeIntRootEdge
Description
A concrete root edge implementation, with int length.
Inheritance
TreeIntRootEdge restricts AbstractRootEdge.
Attributes
| Name | Type | Usage |
| length | xs:integer |
Substructures
- an element called "dict", instance of Dict (0..unbounded).
Definition source
<xs:complexType abstract="false" name="TreeIntRootEdge"> <xs:complexContent> <xs:restriction base="AbstractRootEdge"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="0" name="dict" type="Dict"/> </xs:sequence> <xs:attribute name="length" type="xs:integer"/> </xs:restriction> </xs:complexContent> </xs:complexType>
[ Back to top ]
TreeNode
Description
A concrete node implementation.
Inheritance
TreeNode restricts AbstractNode.
Substructures
- an element called "dict", instance of Dict (0..unbounded).
Definition source
<xs:complexType abstract="false" name="TreeNode"> <xs:complexContent> <xs:restriction base="AbstractNode"> <xs:sequence maxOccurs="1" minOccurs="1"> <xs:element maxOccurs="unbounded" minOccurs="0" name="dict" type="Dict"/> </xs:sequence> </xs:restriction> </xs:complexContent> </xs:complexType>
[ Back to top ]
See also
~/nexml/xsd/trees/tree.xsd includes the following other files:
~/nexml/xsd/trees/tree.xsd is included in:
This page summarizes the contents of schema file "~/nexml/xsd/trees/tree.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 16:26:29 2008.