New in version 2.1.
Nexml module¶
Nexml classes linked to ETE¶
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class
Nexml
(*args, **kargs)¶ Creates a new nexml project.
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build_from_file
(fname, index_otus=True)¶ Populate Nexml project with data in a nexml file.
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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¶
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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.
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superclass
alias of
AbstractChar
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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.
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superclass
alias of
AbstractFormat
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class
AAMapping
(state=None, valueOf_=None) An IUPAC ambiguity mapping.
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superclass
alias of
AbstractMapping
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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.
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superclass
alias of
AbstractObsRow
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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.
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superclass
alias of
AbstractSeqRow
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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.
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superclass
alias of
AbstractObs
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class
AAObsMatrix
(about=None, meta=None, row=None, set=None, valueOf_=None) A matrix of rows with single character observations.
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superclass
alias of
AbstractObsMatrix
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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.
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superclass
alias of
AbstractPolymorphicStateSet
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class
AASeqMatrix
(about=None, meta=None, row=None, set=None, valueOf_=None) A matrix of rows with amino acid data as sequence strings.
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superclass
alias of
AbstractSeqMatrix
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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.
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superclass
alias of
AbstractState
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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.
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superclass
alias of
AbstractStates
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class
AAUncertainStateSet
(about=None, meta=None, label=None, id=None, symbol=None, member=None, valueOf_=None) The AAUncertainStateSet defines an uncertain ambiguity mapping.
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superclass
alias of
AbstractUncertainStateSet
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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.
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superclass
alias of
TaxaLinked
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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.
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superclass
alias of
AbstractBlock
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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.
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superclass
alias of
IDTagged
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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.
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superclass
alias of
IDTagged
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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.
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superclass
alias of
Annotated
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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”.
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superclass
alias of
Base
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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.
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superclass
alias of
IDTagged
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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.
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superclass
alias of
OptionalTaxonLinked
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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).
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superclass
alias of
Labelled
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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.
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superclass
alias of
Annotated
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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.
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superclass
alias of
TaxonLinked
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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.
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superclass
alias of
AbstractUncertainStateSet
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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.
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superclass
alias of
IDTagged
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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.
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superclass
alias of
Annotated
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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.
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superclass
alias of
TaxonLinked
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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.
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superclass
alias of
AbstractBlock
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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.
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superclass
alias of
IDTagged
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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.
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superclass
alias of
IDTagged
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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.
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superclass
alias of
IDTagged
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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.
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superclass
alias of
IDTagged
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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.
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superclass
alias of
AbstractState
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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.
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superclass
alias of
Base
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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.
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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.
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superclass
alias of
AbstractCells
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-
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.
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superclass
alias of
AbstractChar
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class
ContinuousFormat
(about=None, meta=None, states=None, char=None, set=None, valueOf_=None) The ContinuousFormat class is the container of continuous column definitions.
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superclass
alias of
AbstractFormat
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-
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.
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superclass
alias of
AbstractObsRow
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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.
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superclass
alias of
AbstractSeqRow
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-
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.
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superclass
alias of
AbstractObs
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-
class
ContinuousObsMatrix
(about=None, meta=None, row=None, set=None, valueOf_=None) A matrix of rows with single character observations.
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superclass
alias of
AbstractObsMatrix
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class
ContinuousSeqMatrix
(about=None, meta=None, row=None, set=None, valueOf_=None) A matrix of rows with seq strings of type continuous.
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superclass
alias of
AbstractSeqMatrix
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-
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.
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superclass
alias of
AbstractSeqs
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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.
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superclass
alias of
AbstractChar
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class
DNAFormat
(about=None, meta=None, states=None, char=None, set=None, valueOf_=None) The DNAFormat class is the container of DNA column definitions.
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superclass
alias of
AbstractFormat
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-
class
DNAMapping
(state=None, valueOf_=None) An IUPAC ambiguity mapping.
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superclass
alias of
AbstractMapping
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-
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.
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superclass
alias of
AbstractObsRow
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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.
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superclass
alias of
AbstractSeqRow
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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.
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superclass
alias of
AbstractObs
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class
DNAObsMatrix
(about=None, meta=None, row=None, set=None, valueOf_=None) A matrix of rows with single character observations.
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superclass
alias of
AbstractObsMatrix
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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.
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superclass
alias of
AbstractPolymorphicStateSet
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class
DNASeqMatrix
(about=None, meta=None, row=None, set=None, valueOf_=None) A matrix of rows with seq strings of type DNA.
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superclass
alias of
AbstractSeqMatrix
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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.
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superclass
alias of
AbstractState
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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.
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superclass
alias of
AbstractStates
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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.
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superclass
alias of
AbstractUncertainStateSet
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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.
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superclass
alias of
AbstractCells
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-
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.
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superclass
alias of
AbstractSeqs
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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.
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superclass
alias of
AbstractNetwork
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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.
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subclass
alias of
NexmlTree
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superclass
alias of
AbstractTree
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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.
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superclass
alias of
Labelled
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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.
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superclass
alias of
AbstractNetwork
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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.
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subclass
alias of
NexmlTree
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superclass
alias of
AbstractTree
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-
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.
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superclass
alias of
Annotated
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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.
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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.
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superclass
alias of
AbstractEdge
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-
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.
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superclass
alias of
AbstractEdge
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class
NetworkNode
(about=None, meta=None, label=None, id=None, otu=None, root=False, valueOf_=None) A concrete network node implementation.
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superclass
alias of
AbstractNode
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class
Nexml
(*args, **kargs) Creates a new nexml project.
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build_from_file
(fname, index_otus=True) Populate Nexml project with data in a nexml file.
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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.
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superclass
alias of
IDTagged
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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.
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superclass
alias of
AbstractCells
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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.
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superclass
alias of
AbstractSeqs
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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.
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superclass
alias of
AbstractChar
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class
RNAFormat
(about=None, meta=None, states=None, char=None, set=None, valueOf_=None) The RNAFormat class is the container of RNA column definitions.
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superclass
alias of
AbstractFormat
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-
class
RNAMapping
(state=None, valueOf_=None) An IUPAC RNA ambiguity mapping.
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superclass
alias of
AbstractMapping
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-
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.
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superclass
alias of
AbstractObsRow
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-
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.
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superclass
alias of
AbstractSeqRow
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-
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.
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superclass
alias of
AbstractObs
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class
RNAObsMatrix
(about=None, meta=None, row=None, set=None, valueOf_=None) A matrix of rows with single character observations.
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superclass
alias of
AbstractObsMatrix
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-
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.
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superclass
alias of
AbstractPolymorphicStateSet
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-
class
RNASeqMatrix
(about=None, meta=None, row=None, set=None, valueOf_=None) A matrix of rows with seq strings of type RNA.
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superclass
alias of
AbstractSeqMatrix
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-
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.
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superclass
alias of
AbstractState
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-
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.
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superclass
alias of
AbstractStates
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-
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.
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superclass
alias of
AbstractUncertainStateSet
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-
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”.
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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.
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superclass
alias of
AbstractCells
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-
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.
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superclass
alias of
AbstractChar
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class
RestrictionFormat
(about=None, meta=None, states=None, char=None, set=None, valueOf_=None) The RestrictionFormat class is the container of restriction column definitions.
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superclass
alias of
AbstractFormat
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-
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.
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superclass
alias of
AbstractObsRow
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-
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.
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superclass
alias of
AbstractSeqRow
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-
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.
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superclass
alias of
AbstractObs
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-
class
RestrictionObsMatrix
(about=None, meta=None, row=None, set=None, valueOf_=None) A matrix of rows with single character observations.
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superclass
alias of
AbstractObsMatrix
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-
class
RestrictionSeqMatrix
(about=None, meta=None, row=None, set=None, valueOf_=None) A matrix of rows with seq strings of type restriction.
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superclass
alias of
AbstractSeqMatrix
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-
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.
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superclass
alias of
AbstractSeqs
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-
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.
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superclass
alias of
AbstractState
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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.
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superclass
alias of
AbstractStates
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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.
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superclass
alias of
AbstractCells
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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.
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superclass
alias of
AbstractSeqs
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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.
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superclass
alias of
AbstractCells
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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
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superclass
alias of
AbstractChar
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class
StandardFormat
(about=None, meta=None, states=None, char=None, set=None, valueOf_=None) The StandardFormat class is the container of standard column definitions.
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superclass
alias of
AbstractFormat
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class
StandardMapping
(state=None, valueOf_=None) A standard character ambiguity mapping.
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superclass
alias of
AbstractMapping
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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.
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superclass
alias of
AbstractObsRow
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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.
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superclass
alias of
AbstractSeqRow
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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.
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superclass
alias of
AbstractObs
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class
StandardObsMatrix
(about=None, meta=None, row=None, set=None, valueOf_=None) A matrix of rows with single character observations.
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superclass
alias of
AbstractObsMatrix
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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.
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superclass
alias of
AbstractPolymorphicStateSet
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-
class
StandardSeqMatrix
(about=None, meta=None, row=None, set=None, valueOf_=None) A matrix of rows with seq strings of type standard.
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superclass
alias of
AbstractSeqMatrix
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-
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.
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superclass
alias of
AbstractSeqs
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-
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.
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superclass
alias of
AbstractState
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-
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.
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superclass
alias of
AbstractStates
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-
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.
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superclass
alias of
AbstractUncertainStateSet
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-
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.
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superclass
alias of
IDTagged
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-
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.
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superclass
alias of
IDTagged
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-
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.
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superclass
alias of
AbstractEdge
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-
class
TreeFloatRootEdge
(about=None, meta=None, label=None, id=None, length=None, target=None, valueOf_=None) A concrete root edge implementation, with float length.
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superclass
alias of
AbstractRootEdge
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-
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.
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superclass
alias of
AbstractEdge
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-
class
TreeIntRootEdge
(about=None, meta=None, label=None, id=None, length=None, target=None, valueOf_=None) A concrete root edge implementation, with int length.
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superclass
alias of
AbstractRootEdge
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-
class
TreeNode
(about=None, meta=None, label=None, id=None, otu=None, root=False, valueOf_=None) A concrete node implementation.
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superclass
alias of
AbstractNode
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-
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.
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superclass
alias of
TaxaLinked
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-
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.
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class
Nexml
(*args, **kargs) Creates a new nexml project.
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build_from_file
(fname, index_otus=True) Populate Nexml project with data in a nexml file.
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-
class
NexmlTree
(newick=None, alignment=None, alg_format='fasta', sp_naming_function=<function _parse_species>, format=0) Special PhyloTree object with nexml support