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

source code

          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.

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 help(type(x)) 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: __bool__, __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__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

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 help(type(x)) for signature

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
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)