nexml schema 0.9 ~/nexml/xsd/abstract.xsd

Skip to: Site menu | Main content

The future data exchange standard is here!

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

Process nexml data

Schema module documentation

~ / doc / schema-1 / abstract
rss | digg reddit del.icio.us facebook — Last updated: Tue Sep 23 12:49:28 IST 2014

Description

This module defines abstract superclasses. In xml schema, inheritance of complex types is either through extension or through restriction. Extensions in this context means that the child class can have more types of elements appended to the end of its children, and/or more attributes. Restriction means that the child class is more limited than the base class, in that it might have fewer child elements, fewer attributes, or more restricted child element types.

The nexml schema uses inheritance such that abstract superclasses - i.e. those defined in this module - extend each other to form a useful tree of superclasses, from which child classes then derive by restriction. This is done so that for any type there is always an exhaustive abstract superclass, to which parsers should be adapted, so that derived instances won't have surprising substructures.

Other views (open in new window):

organisation chart inheritance tree | file hierarchy inclusions tree | xml schema code schema source

Complex types

Annotated [abstract]

Description

The Annotated complexType is a super class for objects that optionally have metadata annotations of type Meta.

Inheritance

Annotated extends Base. In turn, this type is inherited from by AbstractFormat, AbstractObsMatrix, AbstractSeqMatrix, Labelled, Nexml,

Attributes
Name Type Usage
about xhtml:URIorSafeCURIE optional
Substructures
Definition source
  <xs:complexType abstract="true" mixed="false" name="Annotated">
    <xs:complexContent mixed="false">
      <xs:extension base="Base">
        <xs:sequence>
          <xs:element maxOccurs="unbounded" minOccurs="0" name="meta" type="Meta"/>
        </xs:sequence>
        <xs:attribute name="about" type="xhtml:URIorSafeCURIE" use="optional"/>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>

[ Back to top ]

IDTagged [abstract]

Description

The IDTagged complexType is a super class for objects that require unique id attributes of type xs:ID. The id must be unique within the XML document.

Inheritance

IDTagged extends Labelled. In turn, this type is inherited from by AbstractChar, AbstractEdge, AbstractNetwork, AbstractRootEdge, AbstractSet, AbstractState, AbstractStates, AbstractTree, AbstractTrees, OptionalTaxonLinked, Taxa, TaxaLinked, Taxon, TaxonLinked,

Attributes
Name Type Usage
id xs:ID required
Definition source
  <xs:complexType abstract="true" mixed="false" name="IDTagged">
    <xs:complexContent mixed="false">
      <xs:extension base="Labelled">
        <xs:sequence/>
        <xs:attribute name="id" type="xs:ID" use="required"/>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>

[ Back to top ]

Labelled [abstract]

Description

The Labelled complexType is a super class for objects that optionally have label attributes to use as a (non-unique) name of type xs:string.

Inheritance

Labelled extends Annotated. In turn, this type is inherited from by AbstractObs, IDTagged,

Attributes
Name Type Usage
label xs:string optional
Definition source
  <xs:complexType abstract="true" name="Labelled">
    <xs:complexContent mixed="false">
      <xs:extension base="Annotated">
        <xs:attribute name="label" type="xs:string" use="optional"/>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>

[ Back to top ]

OptionalTaxonLinked [abstract]

Description

The OptionalOTULinked complexType is a super class for objects that that optionally have an otu id reference.

Inheritance

OptionalTaxonLinked extends IDTagged. In turn, this type is inherited from by AbstractNode,

Attributes
Name Type Usage
otu xs:IDREF optional
Definition source
  <xs:complexType abstract="true" name="OptionalTaxonLinked">
    <xs:complexContent>
      <xs:extension base="IDTagged">
        <xs:attribute name="otu" type="xs:IDREF" use="optional"/>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>

[ Back to top ]

TaxaLinked [abstract]

Description

The TaxaLinked complexType is a super class for objects that that require an otus id reference.

Inheritance

TaxaLinked extends IDTagged. In turn, this type is inherited from by AbstractBlock, Trees,

Attributes
Name Type Usage
otus xs:IDREF required
Definition source
  <xs:complexType abstract="true" name="TaxaLinked">
    <xs:complexContent>
      <xs:extension base="IDTagged">
        <xs:attribute name="otus" type="xs:IDREF" use="required"/>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>

[ Back to top ]

TaxonLinked [abstract]

Description

The TaxonLinked complexType is a super class for objects that require a taxon id reference.

Inheritance

TaxonLinked extends IDTagged. In turn, this type is inherited from by AbstractObsRow, AbstractSeqRow,

Attributes
Name Type Usage
otu xs:IDREF required
Definition source
  <xs:complexType abstract="true" name="TaxonLinked">
    <xs:complexContent mixed="false">
      <xs:extension base="IDTagged">
        <xs:attribute name="otu" type="xs:IDREF" use="required"/>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>

[ Back to top ]

See also

~/nexml/xsd/abstract.xsd includes the following other files:

~/nexml/xsd/abstract.xsd is included in:

This page summarizes the contents of schema file "~/nexml/xsd/abstract.xsd". Generated on Tue Sep 23 12:49:33 2014.