Nexml module¶

Nexml classes linked to ETE¶

class Nexml(*args, **kargs)¶

Creates a new nexml project.

build_from_file(fname, index_otus=True)¶

Populate Nexml project with data in a nexml file.

class NexmlTree(newick=None, alignment=None, alg_format='fasta', sp_naming_function=<function _parse_species>, format=0)¶

Special PhyloTree object with nexml support

Generic Nexml classes¶

class AAChar(about=None, meta=None, label=None, id=None, tokens=None, states=None, codon=None, valueOf_=None)

A concrete implementation of the AbstractChar element.

superclass

alias of AbstractChar

class AAFormat(about=None, meta=None, states=None, char=None, set=None, valueOf_=None)

The AAFormat class is the container of amino acid column definitions.

superclass

alias of AbstractFormat

class AAMapping(state=None, valueOf_=None)

An IUPAC ambiguity mapping.

superclass

alias of AbstractMapping

class AAMatrixObsRow(about=None, meta=None, label=None, id=None, otu=None, cell=None, set=None, valueOf_=None)

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

superclass

alias of AbstractObsRow

class AAMatrixSeqRow(about=None, meta=None, label=None, id=None, otu=None, seq=None, valueOf_=None)

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

superclass

alias of AbstractSeqRow

class AAObs(about=None, meta=None, label=None, char=None, state=None, valueOf_=None)

This is a single cell in a matrix containing an amino acid observation.

superclass

alias of AbstractObs

class AAObsMatrix(about=None, meta=None, row=None, set=None, valueOf_=None)

A matrix of rows with single character observations.

superclass

alias of AbstractObsMatrix

class AAPolymorphicStateSet(about=None, meta=None, label=None, id=None, symbol=None, member=None, uncertain_state_set=None, valueOf_=None)

The AAPolymorphicStateSet defines a polymorphic ambiguity mapping.

superclass

alias of AbstractPolymorphicStateSet

class AASeqMatrix(about=None, meta=None, row=None, set=None, valueOf_=None)

A matrix of rows with amino acid data as sequence strings.

superclass

alias of AbstractSeqMatrix

class AAState(about=None, meta=None, label=None, id=None, symbol=None, valueOf_=None)

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.

superclass

alias of AbstractState

class AAStates(about=None, meta=None, label=None, id=None, state=None, polymorphic_state_set=None, uncertain_state_set=None, set=None, valueOf_=None)

A container for a set of states.

superclass

alias of AbstractStates

class AAUncertainStateSet(about=None, meta=None, label=None, id=None, symbol=None, member=None, valueOf_=None)

The AAUncertainStateSet defines an uncertain ambiguity mapping.

superclass

alias of AbstractUncertainStateSet

class AbstractBlock(about=None, meta=None, label=None, id=None, otus=None, format=None, valueOf_=None)

The AbstractBlock is the superclass for blocks that contain an element structure of type AbstractFormat.

superclass

alias of TaxaLinked

class AbstractCells(about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None)

The AbstractSeqBlock type is the superclass for character blocks that consist of granular character state observations.

superclass

alias of AbstractBlock

class AbstractChar(about=None, meta=None, label=None, id=None, tokens=None, states=None, codon=None, valueOf_=None)

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.

superclass

alias of IDTagged

class AbstractEdge(about=None, meta=None, label=None, id=None, source=None, length=None, target=None, valueOf_=None)

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.

superclass

alias of IDTagged

class AbstractFormat(about=None, meta=None, states=None, char=None, set=None, valueOf_=None)

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.

superclass

alias of Annotated

class AbstractMapping(state=None, valueOf_=None)

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”.

superclass

alias of Base

class AbstractNetwork(about=None, meta=None, label=None, id=None, node=None, edge=None, set=None, valueOf_=None)

The AbstractNetwork superclass is what a concrete network inherits from.

superclass

alias of IDTagged

class AbstractNode(about=None, meta=None, label=None, id=None, otu=None, root=False, valueOf_=None)

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.

superclass

alias of OptionalTaxonLinked

class AbstractObs(about=None, meta=None, label=None, char=None, state=None, valueOf_=None)

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).

superclass

alias of Labelled

class AbstractObsMatrix(about=None, meta=None, row=None, set=None, valueOf_=None)

The AbstractObsMatrix super class is the abstract type for a <matrix> element that contains rows which hold granular state observations.

superclass

alias of Annotated

class AbstractObsRow(about=None, meta=None, label=None, id=None, otu=None, cell=None, set=None, valueOf_=None)

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.

superclass

alias of TaxonLinked

class AbstractPolymorphicStateSet(about=None, meta=None, label=None, id=None, symbol=None, member=None, uncertain_state_set=None, valueOf_=None)

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.

superclass

alias of AbstractUncertainStateSet

class AbstractRootEdge(about=None, meta=None, label=None, id=None, length=None, target=None, valueOf_=None)

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.

superclass

alias of IDTagged

class AbstractSeqMatrix(about=None, meta=None, row=None, set=None, valueOf_=None)

The AbstractSeqMatrix super class is the abstract type for a <matrix> element that contains rows which hold raw character sequences.

superclass

alias of Annotated

class AbstractSeqRow(about=None, meta=None, label=None, id=None, otu=None, seq=None, valueOf_=None)

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.

superclass

alias of TaxonLinked

class AbstractSeqs(about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None)

The AbstractSeqBlock type is the superclass for character blocks that consist of raw character sequences.

superclass

alias of AbstractBlock

class AbstractState(about=None, meta=None, label=None, id=None, symbol=None, valueOf_=None)

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.

superclass

alias of IDTagged

class AbstractStates(about=None, meta=None, label=None, id=None, state=None, polymorphic_state_set=None, uncertain_state_set=None, set=None, valueOf_=None)

A container for a set of AbstractState elements.

superclass

alias of IDTagged

class AbstractTree(about=None, meta=None, label=None, id=None, node=None, rootedge=None, edge=None, set=None, valueOf_=None)

The AbstractTree superclass is what a concrete tree inherits from.

superclass

alias of IDTagged

class AbstractTrees(about=None, meta=None, label=None, id=None, network=None, tree=None, set=None, valueOf_=None)

The AbstractTrees superclass is what concrete trees inherit from.

superclass

alias of IDTagged

class AbstractUncertainStateSet(about=None, meta=None, label=None, id=None, symbol=None, member=None, valueOf_=None)

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.

superclass

alias of AbstractState

class Annotated(about=None, meta=None, valueOf_=None)

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

superclass

alias of Base

class Base(valueOf_=None)

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.

class ContinuousCells(about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None)

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

superclass

alias of AbstractCells

class ContinuousChar(about=None, meta=None, label=None, id=None, tokens=None, states=None, codon=None, valueOf_=None)

A concrete implementation of the char element, which requires only an id attribute.

superclass

alias of AbstractChar

class ContinuousFormat(about=None, meta=None, states=None, char=None, set=None, valueOf_=None)

The ContinuousFormat class is the container of continuous column definitions.

superclass

alias of AbstractFormat

class ContinuousMatrixObsRow(about=None, meta=None, label=None, id=None, otu=None, cell=None, set=None, valueOf_=None)

This is a row in a matrix of continuous data as granular obervations.

superclass

alias of AbstractObsRow

class ContinuousMatrixSeqRow(about=None, meta=None, label=None, id=None, otu=None, seq=None, valueOf_=None)

This is a row in a matrix of continuous data as character sequences.

superclass

alias of AbstractSeqRow

class ContinuousObs(about=None, meta=None, label=None, char=None, state=None, valueOf_=None)

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

superclass

alias of AbstractObs

class ContinuousObsMatrix(about=None, meta=None, row=None, set=None, valueOf_=None)

A matrix of rows with single character observations.

superclass

alias of AbstractObsMatrix

class ContinuousSeqMatrix(about=None, meta=None, row=None, set=None, valueOf_=None)

A matrix of rows with seq strings of type continuous.

superclass

alias of AbstractSeqMatrix

class ContinuousSeqs(about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None)

A continuous characters block consisting of float sequences preceded by metadata.

superclass

alias of AbstractSeqs

class DNAChar(about=None, meta=None, label=None, id=None, tokens=None, states=None, codon=None, valueOf_=None)

A concrete implementation of the AbstractChar element.

superclass

alias of AbstractChar

class DNAFormat(about=None, meta=None, states=None, char=None, set=None, valueOf_=None)

The DNAFormat class is the container of DNA column definitions.

superclass

alias of AbstractFormat

class DNAMapping(state=None, valueOf_=None)

An IUPAC ambiguity mapping.

superclass

alias of AbstractMapping

class DNAMatrixObsRow(about=None, meta=None, label=None, id=None, otu=None, cell=None, set=None, valueOf_=None)

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

superclass

alias of AbstractObsRow

class DNAMatrixSeqRow(about=None, meta=None, label=None, id=None, otu=None, seq=None, valueOf_=None)

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

superclass

alias of AbstractSeqRow

class DNAObs(about=None, meta=None, label=None, char=None, state=None, valueOf_=None)

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

superclass

alias of AbstractObs

class DNAObsMatrix(about=None, meta=None, row=None, set=None, valueOf_=None)

A matrix of rows with single character observations.

superclass

alias of AbstractObsMatrix

class DNAPolymorphicStateSet(about=None, meta=None, label=None, id=None, symbol=None, member=None, uncertain_state_set=None, valueOf_=None)

The DNAPolymorphicStateSet type defines an IUPAC ambiguity mapping. It may enclose zero or more AbstractMapping elements to resolve ambiguities.

superclass

alias of AbstractPolymorphicStateSet

class DNASeqMatrix(about=None, meta=None, row=None, set=None, valueOf_=None)

A matrix of rows with seq strings of type DNA.

superclass

alias of AbstractSeqMatrix

class DNAState(about=None, meta=None, label=None, id=None, symbol=None, valueOf_=None)

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.

superclass

alias of AbstractState

class DNAStates(about=None, meta=None, label=None, id=None, state=None, polymorphic_state_set=None, uncertain_state_set=None, set=None, valueOf_=None)

A container for a set of states.

superclass

alias of AbstractStates

class DNAUncertainStateSet(about=None, meta=None, label=None, id=None, symbol=None, member=None, valueOf_=None)

The DNAUncertainStateSet type defines an IUPAC ambiguity mapping. It may enclose zero or more AbstractMapping elements to resolve ambiguities.

superclass

alias of AbstractUncertainStateSet

class DnaCells(about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None)

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

superclass

alias of AbstractCells

class DnaSeqs(about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None)

A DNA characters block consisting of sequences preceded by metadata.

superclass

alias of AbstractSeqs

class FloatNetwork(about=None, meta=None, label=None, id=None, node=None, edge=None, set=None, valueOf_=None)

A concrete network implementation, with floating point edge lengths.

superclass

alias of AbstractNetwork

class FloatTree(about=None, meta=None, label=None, id=None, node=None, rootedge=None, edge=None, set=None, valueOf_=None)

A concrete tree implementation, with floating point edge lengths.

subclass

alias of NexmlTree

superclass

alias of AbstractTree

class IDTagged(about=None, meta=None, label=None, id=None, valueOf_=None)

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.

superclass

alias of Labelled

class IntNetwork(about=None, meta=None, label=None, id=None, node=None, edge=None, set=None, valueOf_=None)

A concrete network implementation, with integer edge lengths.

superclass

alias of AbstractNetwork

class IntTree(about=None, meta=None, label=None, id=None, node=None, rootedge=None, edge=None, set=None, valueOf_=None)

A concrete tree implementation, with integer edge lengths.

subclass

alias of NexmlTree

superclass

alias of AbstractTree

class Labelled(about=None, meta=None, label=None, valueOf_=None)

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.

superclass

alias of Annotated

class LiteralMeta(datatype=None, content=None, property=None, valueOf_=None)

Metadata annotations in which the object is a literal value. If the @content attribute is used, then the element should contain no children.

class NetworkFloatEdge(about=None, meta=None, label=None, id=None, source=None, length=None, target=None, valueOf_=None)

A concrete network edge implementation, with float edge.

superclass

alias of AbstractEdge

class NetworkIntEdge(about=None, meta=None, label=None, id=None, source=None, length=None, target=None, valueOf_=None)

A concrete network edge implementation, with int edge.

superclass

alias of AbstractEdge

class NetworkNode(about=None, meta=None, label=None, id=None, otu=None, root=False, valueOf_=None)

A concrete network node implementation.

superclass

alias of AbstractNode

class Nexml(*args, **kargs)

Creates a new nexml project.

build_from_file(fname, index_otus=True)

Populate Nexml project with data in a nexml file.

class OptionalTaxonLinked(about=None, meta=None, label=None, id=None, otu=None, valueOf_=None)

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

superclass

alias of IDTagged

class ProteinCells(about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None)

An amino acid characters block consisting of granular cells preceded by metadata.

superclass

alias of AbstractCells

class ProteinSeqs(about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None)

An amino acid characters block consisting of sequences preceded by metadata.

superclass

alias of AbstractSeqs

class RNAChar(about=None, meta=None, label=None, id=None, tokens=None, states=None, codon=None, valueOf_=None)

A concrete implementation of the AbstractChar element, i.e. a single column in an alignment.

superclass

alias of AbstractChar

class RNAFormat(about=None, meta=None, states=None, char=None, set=None, valueOf_=None)

The RNAFormat class is the container of RNA column definitions.

superclass

alias of AbstractFormat

class RNAMapping(state=None, valueOf_=None)

An IUPAC RNA ambiguity mapping.

superclass

alias of AbstractMapping

class RNAMatrixObsRow(about=None, meta=None, label=None, id=None, otu=None, cell=None, set=None, valueOf_=None)

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

superclass

alias of AbstractObsRow

class RNAMatrixSeqRow(about=None, meta=None, label=None, id=None, otu=None, seq=None, valueOf_=None)

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

superclass

alias of AbstractSeqRow

class RNAObs(about=None, meta=None, label=None, char=None, state=None, valueOf_=None)

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

superclass

alias of AbstractObs

class RNAObsMatrix(about=None, meta=None, row=None, set=None, valueOf_=None)

A matrix of rows with single character observations.

superclass

alias of AbstractObsMatrix

class RNAPolymorphicStateSet(about=None, meta=None, label=None, id=None, symbol=None, member=None, uncertain_state_set=None, valueOf_=None)

The RNAPolymorphicStateSet describes a single polymorphic IUPAC ambiguity mapping.

superclass

alias of AbstractPolymorphicStateSet

class RNASeqMatrix(about=None, meta=None, row=None, set=None, valueOf_=None)

A matrix of rows with seq strings of type RNA.

superclass

alias of AbstractSeqMatrix

class RNAState(about=None, meta=None, label=None, id=None, symbol=None, valueOf_=None)

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.

superclass

alias of AbstractState

class RNAStates(about=None, meta=None, label=None, id=None, state=None, polymorphic_state_set=None, uncertain_state_set=None, set=None, valueOf_=None)

A container for a set of states.

superclass

alias of AbstractStates

class RNAUncertainStateSet(about=None, meta=None, label=None, id=None, symbol=None, member=None, valueOf_=None)

The RNAUncertainStateSet describes a single uncertain IUPAC ambiguity mapping.

superclass

alias of AbstractUncertainStateSet

class ResourceMeta(href=None, rel=None, meta=None, valueOf_=None)

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”.

class RestrictionCells(about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None)

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

superclass

alias of AbstractCells

class RestrictionChar(about=None, meta=None, label=None, id=None, tokens=None, states=None, codon=None, valueOf_=None)

A concrete implementation of the char element, which requires a unique identifier and a state set reference.

superclass

alias of AbstractChar

class RestrictionFormat(about=None, meta=None, states=None, char=None, set=None, valueOf_=None)

The RestrictionFormat class is the container of restriction column definitions.

superclass

alias of AbstractFormat

class RestrictionMatrixObsRow(about=None, meta=None, label=None, id=None, otu=None, cell=None, set=None, valueOf_=None)

This is a row in a matrix of restriction site data as granular obervations.

superclass

alias of AbstractObsRow

class RestrictionMatrixSeqRow(about=None, meta=None, label=None, id=None, otu=None, seq=None, valueOf_=None)

This is a row in a matrix of restriction site data as character sequences.

superclass

alias of AbstractSeqRow

class RestrictionObs(about=None, meta=None, label=None, char=None, state=None, valueOf_=None)

This is a single cell in a matrix containing a restriction site observation.

superclass

alias of AbstractObs

class RestrictionObsMatrix(about=None, meta=None, row=None, set=None, valueOf_=None)

A matrix of rows with single character observations.

superclass

alias of AbstractObsMatrix

class RestrictionSeqMatrix(about=None, meta=None, row=None, set=None, valueOf_=None)

A matrix of rows with seq strings of type restriction.

superclass

alias of AbstractSeqMatrix

class RestrictionSeqs(about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None)

A restriction site characters block consisting of sequences preceded by metadata.

superclass

alias of AbstractSeqs

class RestrictionState(about=None, meta=None, label=None, id=None, symbol=None, valueOf_=None)

This is a concrete implementation of the state element, which requires a symbol element, in this case restricted to 0/1.

superclass

alias of AbstractState

class RestrictionStates(about=None, meta=None, label=None, id=None, state=None, polymorphic_state_set=None, uncertain_state_set=None, set=None, valueOf_=None)

A container for a set of states.

superclass

alias of AbstractStates

class RnaCells(about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None)

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

superclass

alias of AbstractCells

class RnaSeqs(about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None)

A RNA characters block consisting of sequences preceded by metadata.

superclass

alias of AbstractSeqs

class StandardCells(about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None)

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

superclass

alias of AbstractCells

class StandardChar(about=None, meta=None, label=None, id=None, tokens=None, states=None, codon=None, valueOf_=None)

A concrete implementation of the char element, which requires a states attribute to refer to a set of defined states

superclass

alias of AbstractChar

class StandardFormat(about=None, meta=None, states=None, char=None, set=None, valueOf_=None)

The StandardFormat class is the container of standard column definitions.

superclass

alias of AbstractFormat

class StandardMapping(state=None, valueOf_=None)

A standard character ambiguity mapping.

superclass

alias of AbstractMapping

class StandardMatrixObsRow(about=None, meta=None, label=None, id=None, otu=None, cell=None, set=None, valueOf_=None)

This is a row in a matrix of standard data as granular obervations.

superclass

alias of AbstractObsRow

class StandardMatrixSeqRow(about=None, meta=None, label=None, id=None, otu=None, seq=None, valueOf_=None)

This is a row in a matrix of standard data as character sequences.

superclass

alias of AbstractSeqRow

class StandardObs(about=None, meta=None, label=None, char=None, state=None, valueOf_=None)

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

superclass

alias of AbstractObs

class StandardObsMatrix(about=None, meta=None, row=None, set=None, valueOf_=None)

A matrix of rows with single character observations.

superclass

alias of AbstractObsMatrix

class StandardPolymorphicStateSet(about=None, meta=None, label=None, id=None, symbol=None, member=None, uncertain_state_set=None, valueOf_=None)

The StandardPolymorphicStateSet type is a single polymorphic ambiguity mapping.

superclass

alias of AbstractPolymorphicStateSet

class StandardSeqMatrix(about=None, meta=None, row=None, set=None, valueOf_=None)

A matrix of rows with seq strings of type standard.

superclass

alias of AbstractSeqMatrix

class StandardSeqs(about=None, meta=None, label=None, id=None, otus=None, format=None, matrix=None, valueOf_=None)

A standard characters block consisting of sequences preceded by metadata.

superclass

alias of AbstractSeqs

class StandardState(about=None, meta=None, label=None, id=None, symbol=None, valueOf_=None)

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.

superclass

alias of AbstractState

class StandardStates(about=None, meta=None, label=None, id=None, state=None, polymorphic_state_set=None, uncertain_state_set=None, set=None, valueOf_=None)

A container for a set of states.

superclass

alias of AbstractStates

class StandardUncertainStateSet(about=None, meta=None, label=None, id=None, symbol=None, member=None, valueOf_=None)

The StandardUncertainStateSet type is a single uncertain ambiguity mapping.

superclass

alias of AbstractUncertainStateSet

class TaxaLinked(about=None, meta=None, label=None, id=None, otus=None, valueOf_=None)

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

superclass

alias of IDTagged

class TaxonLinked(about=None, meta=None, label=None, id=None, otu=None, valueOf_=None)

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

superclass

alias of IDTagged

class TreeFloatEdge(about=None, meta=None, label=None, id=None, source=None, length=None, target=None, valueOf_=None)

A concrete edge implementation, with float length.

superclass

alias of AbstractEdge

class TreeFloatRootEdge(about=None, meta=None, label=None, id=None, length=None, target=None, valueOf_=None)

A concrete root edge implementation, with float length.

superclass

alias of AbstractRootEdge

class TreeIntEdge(about=None, meta=None, label=None, id=None, source=None, length=None, target=None, valueOf_=None)

A concrete edge implementation, with int length.

superclass

alias of AbstractEdge

class TreeIntRootEdge(about=None, meta=None, label=None, id=None, length=None, target=None, valueOf_=None)

A concrete root edge implementation, with int length.

superclass

alias of AbstractRootEdge

class TreeNode(about=None, meta=None, label=None, id=None, otu=None, root=False, valueOf_=None)

A concrete node implementation.

superclass

alias of AbstractNode

class Trees(about=None, meta=None, label=None, id=None, otus=None, network=None, tree=None, set=None, valueOf_=None)

A concrete container for tree objects.

superclass

alias of TaxaLinked

class attrExtensions(valueOf_=None)

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.

class Nexml(*args, **kargs)

Creates a new nexml project.

build_from_file(fname, index_otus=True)

Populate Nexml project with data in a nexml file.

class NexmlTree(newick=None, alignment=None, alg_format='fasta', sp_naming_function=<function _parse_species>, format=0)

Special PhyloTree object with nexml support