Package Bio :: Package Phylo :: Module PhyloXML :: Class Phylogeny

Class Phylogeny

          object --+        
                   |        
BaseTree.TreeElement --+    
                       |    
            PhyloElement --+
                           |
          object --+       |
                   |       |
BaseTree.TreeElement --+   |
                       |   |
          object --+   |   |
                   |   |   |
  BaseTree.TreeMixin --+   |
                       |   |
           BaseTree.Tree --+
                           |
                          Phylogeny

A phylogenetic tree.

:Parameters:
    root : Clade
        the root node/clade of this tree
    rooted : bool
        True if this tree is rooted
    rerootable : bool
        True if this tree is rerootable
    branch_length_unit : string
        unit for branch_length values on clades
    name : string
        identifier for this tree, not required to be unique
    id : Id
        unique identifier for this tree
    description : string
        plain-text description
    date : Date
        date for the root node of this tree
    confidences : list
        Confidence objects for this tree
    clade_relations : list
        CladeRelation objects
    sequence_relations : list 
        SequenceRelation objects
    properties : list
        Property objects
    other : list
        non-phyloXML elements (type `Other`)

Instance Methods

[hide private]

__init__(self, root=None, rooted=True, rerootable=None, branch_length_unit=None, type=None, name=None, id=None, description=None, date=None, confidences=None, clade_relations=None, sequence_relations=None, properties=None, other=None)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

source code

as_phyloxml(self)
Return this tree, a PhyloXML-compatible Phylogeny object.

source code

to_phyloxml_container(self, **kwargs)
Create a new Phyloxml object containing just this phylogeny.

source code

to_alignment(self)
Construct an alignment from the aligned sequences in this tree.

source code

_get_confidence(self)
Equivalent to self.confidences[0] if there is only 1 value.

source code

_set_confidence(self, value)

source code

_del_confidence(self)

source code

Inherited from BaseTree.Tree: __format__, __str__, format, is_terminal, root_with_outgroup

Inherited from BaseTree.TreeElement: __repr__

Inherited from BaseTree.TreeMixin: collapse, collapse_all, common_ancestor, count_terminals, depths, distance, find_any, find_clades, find_elements, get_nonterminals, get_path, get_terminals, is_bifurcating, is_monophyletic, is_parent_of, is_preterminal, ladderize, prune, split, total_branch_length, trace

Inherited from BaseTree.TreeMixin (private): _filter_search

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__

Class Methods

[hide private]

from_tree(cls, tree, **kwargs)
Create a new Phylogeny given a Tree (from Newick/Nexus or BaseTree).

source code

from_clade(cls, clade, **kwargs)
Create a new Phylogeny given a Newick or BaseTree Clade object.

source code

Inherited from BaseTree.Tree: randomized

Properties

[hide private]

confidence
Equivalent to self.confidences[0] if there is only 1 value.

Inherited from BaseTree.Tree: clade

Inherited from object: __class__

Method Details

[hide private]

init(self, root=None, rooted=True, rerootable=None, branch_length_unit=None, type=None, name=None, id=None, description=None, date=None, confidences=None, clade_relations=None, sequence_relations=None, properties=None, other=None)
(Constructor)

source code

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__: (inherited documentation)

from_tree(cls, tree, **kwargs)
Class Method

source code

Create a new Phylogeny given a Tree (from Newick/Nexus or BaseTree).

Keyword arguments are the usual `Phylogeny` constructor parameters.

from_clade(cls, clade, **kwargs)
Class Method

source code

Create a new Phylogeny given a Newick or BaseTree Clade object.

Keyword arguments are the usual `PhyloXML.Clade` constructor parameters.

Overrides: BaseTree.Tree.from_clade

as_phyloxml(self)

source code

Return this tree, a PhyloXML-compatible Phylogeny object.

Overrides the `BaseTree` method.

Overrides: BaseTree.Tree.as_phyloxml

_get_confidence(self)

source code

Equivalent to self.confidences[0] if there is only 1 value.

See also: `Clade.confidence`, `Clade.taxonomy`

Property Details

[hide private]

confidence

Equivalent to self.confidences[0] if there is only 1 value.

See also: `Clade.confidence`, `Clade.taxonomy`

Get Method:: _get_confidence(self) - Equivalent to self.confidences[0] if there is only 1 value.
Set Method:: _set_confidence(self, value)
Delete Method:: _del_confidence(self)

Class Phylogeny

__init__(self, root=None, rooted=True, rerootable=None, branch_length_unit=None, type=None, name=None, id=None, description=None, date=None, confidences=None, clade_relations=None, sequence_relations=None, properties=None, other=None) (Constructor)

from_tree(cls, tree, **kwargs) Class Method

from_clade(cls, clade, **kwargs) Class Method

as_phyloxml(self)

_get_confidence(self)

confidence

init(self, root=None, rooted=True, rerootable=None, branch_length_unit=None, type=None, name=None, id=None, description=None, date=None, confidences=None, clade_relations=None, sequence_relations=None, properties=None, other=None)
(Constructor)

from_tree(cls, tree, **kwargs)
Class Method

from_clade(cls, clade, **kwargs)
Class Method