Package Bio :: Package Phylo :: Module PhyloXML :: Class Clade

Class Clade

          object --+        
                   |        
BaseTree.TreeElement --+    
                       |    
            PhyloElement --+
                           |
          object --+       |
                   |       |
BaseTree.TreeElement --+   |
                       |   |
          object --+   |   |
                   |   |   |
  BaseTree.TreeMixin --+   |
                       |   |
          BaseTree.Clade --+
                           |
                          Clade

Describes a branch of the current phylogenetic tree.

Used recursively, describes the topology of a phylogenetic tree.

Both ``color`` and ``width`` elements should be interpreted by client code
as applying to the whole clade, including all descendents, unless
overwritten in-sub clades. This module doesn't automatically assign these
attributes to sub-clades to achieve this cascade -- and neither should you.

:Parameters:
    branch_length
        parent branch length of this clade
    id_source
        link other elements to a clade (on the xml-level)
    name : string
        short label for this clade
    confidences : list of Confidence objects
        used to indicate the support for a clade/parent branch.
    width : float
        branch width for this clade (including branch from parent)
    color : BranchColor
        color used for graphical display of this clade
    node_id
        unique identifier for the root node of this clade
    taxonomies : list
        Taxonomy objects
    sequences : list
        Sequence objects
    events : Events
        describe such events as gene-duplications at the root node/parent
        branch of this clade
    binary_characters : BinaryCharacters
        binary characters
    distributions : list of Distribution objects
        distribution(s) of this clade
    date : Date
        a date for the root node of this clade
    references : list
        Reference objects
    properties : list
        Property objects
    clades : list Clade objects
        Sub-clades
    other : list of Other objects
        non-phyloXML objects

Instance Methods

[hide private]

__init__(self, branch_length=None, id_source=None, name=None, width=None, color=None, node_id=None, events=None, binary_characters=None, date=None, confidences=None, taxonomies=None, sequences=None, distributions=None, references=None, properties=None, clades=None, other=None)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

source code

to_phylogeny(self, **kwargs)
Create a new phylogeny containing just this clade.

source code

_get_confidence(self)

source code

_set_confidence(self, value)

source code

_del_confidence(self)

source code

_get_taxonomy(self)

source code

_set_taxonomy(self, value)

source code

Inherited from BaseTree.Clade: __getitem__, __iter__, __len__, __nonzero__, __str__, is_terminal

Inherited from BaseTree.Clade (private): _get_color, _set_color

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_clade(cls, clade, **kwargs)
Create a new PhyloXML Clade from a Newick or BaseTree Clade object.

source code

Properties

[hide private]

confidence

taxonomy

Inherited from BaseTree.Clade: color, root

Inherited from object: __class__

Method Details

[hide private]

init(self, branch_length=None, id_source=None, name=None, width=None, color=None, node_id=None, events=None, binary_characters=None, date=None, confidences=None, taxonomies=None, sequences=None, distributions=None, references=None, properties=None, clades=None, other=None)
(Constructor)

source code

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

Overrides: object.__init__: (inherited documentation)

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

source code

Create a new PhyloXML Clade from a Newick or BaseTree Clade object.

Keyword arguments are the usual PhyloXML Clade constructor parameters.

Property Details

[hide private]

confidence

Get Method:: _get_confidence(self)
Set Method:: _set_confidence(self, value)
Delete Method:: _del_confidence(self)

taxonomy

Get Method:: _get_taxonomy(self)
Set Method:: _set_taxonomy(self, value)

Class Clade

__init__(self, branch_length=None, id_source=None, name=None, width=None, color=None, node_id=None, events=None, binary_characters=None, date=None, confidences=None, taxonomies=None, sequences=None, distributions=None, references=None, properties=None, clades=None, other=None) (Constructor)

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

confidence

taxonomy

init(self, branch_length=None, id_source=None, name=None, width=None, color=None, node_id=None, events=None, binary_characters=None, date=None, confidences=None, taxonomies=None, sequences=None, distributions=None, references=None, properties=None, clades=None, other=None)
(Constructor)

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