New in version 2.1.
Creates a new nexml project.
Populate Nexml project with data in a nexml file.
Special PhyloTree object with nexml support
A concrete implementation of the AbstractChar element.
alias of AbstractChar
The AAFormat class is the container of amino acid column definitions.
alias of AbstractFormat
An IUPAC ambiguity mapping.
alias of AbstractMapping
This is a row in a matrix of amino acid data containing granular observations.
alias of AbstractObsRow
This is a row in a matrix of amino acid data containing raw sequence data.
alias of AbstractSeqRow
This is a single cell in a matrix containing an amino acid observation.
alias of AbstractObs
A matrix of rows with single character observations.
alias of AbstractObsMatrix
The AAPolymorphicStateSet defines a polymorphic ambiguity mapping.
alias of AbstractPolymorphicStateSet
A matrix of rows with amino acid data as sequence strings.
alias of AbstractSeqMatrix
This is a concrete implementation of the state element, which requires a symbol element, in this case restricted to AAToken, i.e. a single IUPAC amino acid symbol, and optional mapping elements to refer to other states.
alias of AbstractState
A container for a set of states.
alias of AbstractStates
The AAUncertainStateSet defines an uncertain ambiguity mapping.
alias of AbstractUncertainStateSet
The AbstractBlock is the superclass for blocks that contain an element structure of type AbstractFormat.
alias of TaxaLinked
The AbstractSeqBlock type is the superclass for character blocks that consist of granular character state observations.
alias of AbstractBlock
The AbstractChar type is the superclass for a column definition, which may have a “states” attribute that refers to an AbstractStates element, a codon attribute of type CodonPosition and an id attribute that may be an actual id (e.g. for categorical matrices where observations explicitly refer to a column definition) or an integer for sequence matrices.
alias of IDTagged
The AbstractEdge superclass is what concrete edges inherit from by restriction. It represents an edge element much like that of GraphML, i.e. an element that connects node elements.
alias of IDTagged
The AbstractFormat type is the superclass for the element that defines the allowed characters and states in a matrix, and their ambiguity mapping. It may enclose AbstractStates elements that define states and their mappings, and AbstractChar elements that specify which AbstractStates apply to which matrix columns.
alias of Annotated
The AbstractMapping type is the superclass for an ambiguity mapping. In an instance document, a subclass of this type will look like <member state=”st1”/>, i.e. an element called “member” with an attribute called “state” whose value is an id reference that refers to an element that subclasses AbstractState. The purpose of AbstractMapping is to specify which other states may be implied, e.g. a nucleotide symbol “N” would have mappings to “A”, “C”, “G” and “T”.
alias of Base
The AbstractNetwork superclass is what a concrete network inherits from.
alias of IDTagged
The AbstractNode superclass is what concrete nodes inherit from by restriction. It represents a node element much like that of GraphML, i.e. an element that is connected into a tree by edge elements.
alias of OptionalTaxonLinked
The AbstractObs type is the superclass for single observations, i.e. cells in a matrix. A concrete instance of AbstractObs has a “char” attribute that refers to an explicitly defined character (e.g. in categorical matrices), and a “state” attribute that either holds a reference to an explicitly defined state, or a raw state value (a continuous value).
alias of Labelled
The AbstractObsMatrix super class is the abstract type for a <matrix> element that contains rows which hold granular state observations.
alias of Annotated
The AbstractObsRow represents a single row in a matrix. The row must refer to a previously declared otu element by its id attribute (and must have an id itself, may have a label, and may have meta attachments). The row contains multiple cell elements.
alias of TaxonLinked
The AbstractPolymorphicStateSet type is the super-class for a polymorphic state set definition. The element has a required AbstractSymbol attribute 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.
alias of AbstractUncertainStateSet
The AbstractRootEdge complex type is a superclass for the edge that leads into a root, i.e. an edge with only a target attribute, but no source attribute. This type of edge is used for coalescent trees, where the initial lineage has a certain length before things start splitting up.
alias of IDTagged
The AbstractSeqMatrix super class is the abstract type for a <matrix> element that contains rows which hold raw character sequences.
alias of Annotated
The AbstractSeqRow represents a single row in a matrix. The row must refer to a previously declared otu element by its id attribute (and must have an id itself, may have a label, and may have meta attachments). The row contains a single seq element with raw character data.
alias of TaxonLinked
The AbstractSeqBlock type is the superclass for character blocks that consist of raw character sequences.
alias of AbstractBlock
The AbstractState type is the super-class for a state definition. The element has a required symbol attribute 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.
alias of IDTagged
A container for a set of AbstractState elements.
alias of IDTagged
The AbstractTree superclass is what a concrete tree inherits from.
alias of IDTagged
The AbstractTrees superclass is what concrete trees inherit from.
alias of IDTagged
The AbstractUncertainStateSet type is the super-class for an uncertain state set definition. The element has a required AbstractSymbol attribute 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.
alias of AbstractState
The Annotated complexType is a super class for objects that optionally have metadata annotations of type Meta.
alias of Base
The base type for all complexType definitions in the nexml schema. This type allows a number of special attributes: xml:lang - for languages codes xml:base - see http://www.w3.org/TR/xmlbase/ xml:id - see http://www.w3.org/TR/xml-id/ xml:space - for whitespace handling xlink:href - for links Also see http://www.w3.org/2001/xml.xsd for more information on the xml and xlink attributes.
A continuous characters block consisting of granular cells preceded by metadata.
alias of AbstractCells
A concrete implementation of the char element, which requires only an id attribute.
alias of AbstractChar
The ContinuousFormat class is the container of continuous column definitions.
alias of AbstractFormat
This is a row in a matrix of continuous data as granular obervations.
alias of AbstractObsRow
This is a row in a matrix of continuous data as character sequences.
alias of AbstractSeqRow
This is a single cell in a matrix containing a continuous observation.
alias of AbstractObs
A matrix of rows with single character observations.
alias of AbstractObsMatrix
A matrix of rows with seq strings of type continuous.
alias of AbstractSeqMatrix
A continuous characters block consisting of float sequences preceded by metadata.
alias of AbstractSeqs
A concrete implementation of the AbstractChar element.
alias of AbstractChar
The DNAFormat class is the container of DNA column definitions.
alias of AbstractFormat
An IUPAC ambiguity mapping.
alias of AbstractMapping
This is a row in a matrix of DNA data containing granular observations.
alias of AbstractObsRow
This is a row in a matrix of DNA data containing raw sequence data.
alias of AbstractSeqRow
This is a single cell in a matrix containing a nucleotide observation.
alias of AbstractObs
A matrix of rows with single character observations.
alias of AbstractObsMatrix
The DNAPolymorphicStateSet type defines an IUPAC ambiguity mapping. It may enclose zero or more AbstractMapping elements to resolve ambiguities.
alias of AbstractPolymorphicStateSet
A matrix of rows with seq strings of type DNA.
alias of AbstractSeqMatrix
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.
alias of AbstractState
A container for a set of states.
alias of AbstractStates
The DNAUncertainStateSet type defines an IUPAC ambiguity mapping. It may enclose zero or more AbstractMapping elements to resolve ambiguities.
alias of AbstractUncertainStateSet
A DNA characters block consisting of granular cells preceded by metadata.
alias of AbstractCells
A DNA characters block consisting of sequences preceded by metadata.
alias of AbstractSeqs
A concrete network implementation, with floating point edge lengths.
alias of AbstractNetwork
A concrete tree implementation, with floating point edge lengths.
alias of NexmlTree
alias of AbstractTree
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.
alias of Labelled
A concrete network implementation, with integer edge lengths.
alias of AbstractNetwork
A concrete tree implementation, with integer edge lengths.
alias of NexmlTree
alias of AbstractTree
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.
alias of Annotated
Metadata annotations in which the object is a literal value. If the @content attribute is used, then the element should contain no children.
A concrete network edge implementation, with float edge.
alias of AbstractEdge
A concrete network edge implementation, with int edge.
alias of AbstractEdge
A concrete network node implementation.
alias of AbstractNode
Creates a new nexml project.
Populate Nexml project with data in a nexml file.
The OptionalOTULinked complexType is a super class for objects that that optionally have an otu id reference.
alias of IDTagged
An amino acid characters block consisting of granular cells preceded by metadata.
alias of AbstractCells
An amino acid characters block consisting of sequences preceded by metadata.
alias of AbstractSeqs
A concrete implementation of the AbstractChar element, i.e. a single column in an alignment.
alias of AbstractChar
The RNAFormat class is the container of RNA column definitions.
alias of AbstractFormat
An IUPAC RNA ambiguity mapping.
alias of AbstractMapping
This is a row in a matrix of RNA data containing granular observations.
alias of AbstractObsRow
This is a row in a matrix of RNA data containing raw sequence data.
alias of AbstractSeqRow
This is a single cell in a matrix containing an RNA nucleotide observation.
alias of AbstractObs
A matrix of rows with single character observations.
alias of AbstractObsMatrix
The RNAPolymorphicStateSet describes a single polymorphic IUPAC ambiguity mapping.
alias of AbstractPolymorphicStateSet
A matrix of rows with seq strings of type RNA.
alias of AbstractSeqMatrix
This is a concrete implementation of the state element, which requires a symbol attribute, in this case restricted to RNAToken, i.e. a single IUPAC nucleotide symbol, and optional mapping elements to refer to other states.
alias of AbstractState
A container for a set of states.
alias of AbstractStates
The RNAUncertainStateSet describes a single uncertain IUPAC ambiguity mapping.
alias of AbstractUncertainStateSet
Metadata annotations in which the object is a resource. If this element contains meta elements as children, then the object of this annotation is a “blank node”.
A standard characters block consisting of granular cells preceded by metadata.
alias of AbstractCells
A concrete implementation of the char element, which requires a unique identifier and a state set reference.
alias of AbstractChar
The RestrictionFormat class is the container of restriction column definitions.
alias of AbstractFormat
This is a row in a matrix of restriction site data as granular obervations.
alias of AbstractObsRow
This is a row in a matrix of restriction site data as character sequences.
alias of AbstractSeqRow
This is a single cell in a matrix containing a restriction site observation.
alias of AbstractObs
A matrix of rows with single character observations.
alias of AbstractObsMatrix
A matrix of rows with seq strings of type restriction.
alias of AbstractSeqMatrix
A restriction site characters block consisting of sequences preceded by metadata.
alias of AbstractSeqs
This is a concrete implementation of the state element, which requires a symbol element, in this case restricted to 0/1.
alias of AbstractState
A container for a set of states.
alias of AbstractStates
A RNA characters block consisting of granular cells preceded by metadata.
alias of AbstractCells
A RNA characters block consisting of sequences preceded by metadata.
alias of AbstractSeqs
A standard characters block consisting of granular cells preceded by metadata.
alias of AbstractCells
A concrete implementation of the char element, which requires a states attribute to refer to a set of defined states
alias of AbstractChar
The StandardFormat class is the container of standard column definitions.
alias of AbstractFormat
A standard character ambiguity mapping.
alias of AbstractMapping
This is a row in a matrix of standard data as granular obervations.
alias of AbstractObsRow
This is a row in a matrix of standard data as character sequences.
alias of AbstractSeqRow
This is a single cell in a matrix containing a standard observation.
alias of AbstractObs
A matrix of rows with single character observations.
alias of AbstractObsMatrix
The StandardPolymorphicStateSet type is a single polymorphic ambiguity mapping.
alias of AbstractPolymorphicStateSet
A matrix of rows with seq strings of type standard.
alias of AbstractSeqMatrix
A standard characters block consisting of sequences preceded by metadata.
alias of AbstractSeqs
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.
alias of AbstractState
A container for a set of states.
alias of AbstractStates
The StandardUncertainStateSet type is a single uncertain ambiguity mapping.
alias of AbstractUncertainStateSet
The TaxaLinked complexType is a super class for objects that that require an otus id reference.
alias of IDTagged
The TaxonLinked complexType is a super class for objects that require a taxon id reference.
alias of IDTagged
A concrete edge implementation, with float length.
alias of AbstractEdge
A concrete root edge implementation, with float length.
alias of AbstractRootEdge
A concrete edge implementation, with int length.
alias of AbstractEdge
A concrete root edge implementation, with int length.
alias of AbstractRootEdge
A concrete node implementation.
alias of AbstractNode
A concrete container for tree objects.
alias of TaxaLinked
This element is for use in WSDL 1.1 only. It does not apply to WSDL 2.0 documents. Use in WSDL 2.0 documents is invalid.
Creates a new nexml project.
Populate Nexml project with data in a nexml file.
Special PhyloTree object with nexml support