Package Bio :: Package Phylo :: Module BaseTree :: Class Clade
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Class Clade

source code

 object --+    
          |    
TreeElement --+
              |
 object --+   |
          |   |
  TreeMixin --+
              |
             Clade
Known Subclasses:

A recursively defined sub-tree.
Instance Methods [hide private]
 
__init__(self, branch_length=None, name=None, clades=None, confidence=None, color=None, width=None)
x.__init__(...) initializes x; see help(type(x)) for signature
source code
 
is_terminal(self)
True if this is a terminal (leaf) node.
source code
 
__getitem__(self, index)
Get clades by index (integer or slice).
source code
 
__iter__(self)
Iterate through this tree's direct descendent clades (sub-trees).
source code
 
__len__(self)
Number of clades directy under the root.
source code
 
__bool__(self)
Boolean value of an instance of this class (True).
source code
 
__nonzero__(self)
Boolean value of an instance of this class (True).
source code
 
__str__(self)
Show this object's constructor with its primitive arguments.
source code
 
_get_color(self) source code
 
_set_color(self, arg) source code

Inherited from TreeElement: __repr__

Inherited from 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 TreeMixin (private): _filter_search

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

Properties [hide private]
  root
Allow TreeMixin methods to traverse clades properly.
  color
Branch color.

Inherited from object: __class__

Method Details [hide private]

__init__(self, branch_length=None, name=None, clades=None, confidence=None, color=None, width=None)
(Constructor)

source code 
x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:
  • branch_length (str) - The length of the branch leading to the root node of this clade.
  • name (str) - The clade's name (a label).
  • clades (list) - Sub-trees rooted directly under this tree's root.
  • confidence (number) - Support.
  • color (BranchColor) - The display color of the branch and descendents.
  • width (number) - The display width of the branch and descendents.
Overrides: object.__init__
(inherited documentation)

__bool__(self)

source code 

Boolean value of an instance of this class (True).

NB: If this method is not defined, but __len__ is, then the object is considered true if the result of __len__() is nonzero. We want Clade instances to always be considered True.

__nonzero__(self)
(Boolean test operator)

source code 

Boolean value of an instance of this class (True).

NB: If this method is not defined, but __len__ is, then the object is considered true if the result of __len__() is nonzero. We want Clade instances to always be considered True.

__str__(self)
(Informal representation operator)

source code 
Show this object's constructor with its primitive arguments.
Overrides: object.__str__
(inherited documentation)

Property Details [hide private]

root

Allow TreeMixin methods to traverse clades properly.
Get Method:
unreachable.root(self) - Allow TreeMixin methods to traverse clades properly.

color

Branch color.
Get Method:
_get_color(self)
Set Method:
_set_color(self, arg)