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__init__(self,
newick=None,
text_array=None,
fdist=<function spearman_dist at 0x14741b8>)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature |
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iter_leaf_profiles(self)
Returns an iterator over all the profiles associated to the leaves
under this node. |
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get_leaf_profiles(self)
Returns the list of all the profiles associated to the leaves under
this node. |
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get_dunn(self,
clusters,
fdist=None)
Calculates the Dunn index for the given set of descendant nodes. |
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_calculate_avg_profile(self)
This internal function updates the mean profile associated to an
internal node. |
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Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__subclasshook__
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__add__(self,
value)
This allows to sum two trees. |
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__and__(self,
value)
This allows to execute tree&'A' to obtain the descendant node A |
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__len__(self)
Node len returns number of children. |
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_asciiArt(self,
char1=' - ' ,
show_internal=True,
compact=False)
Returns the ASCII representation of the tree. |
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_iter_descendants_postorder(self)
Iterator over all desdecendant nodes. |
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_iter_descendants_preorder(self)
Iterator over all desdecendant nodes. |
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add_child(self,
child=None,
name=None,
dist=None,
support=None)
Adds a new child to this node. |
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add_feature(self,
pr_name,
pr_value)
Adds or updates a node's feature. |
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add_features(self,
**features)
Adds or updates a node's feature. |
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del_feature(self,
pr_name)
Deletes permanently a node's feature. |
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delete(self,
prevent_nondicotomic=True)
Deletes node from the tree structure. |
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describe(self)
Prints general information about this node and its connections. |
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detach(self)
Detachs this node (and all its descendants) from its parent and
returns the referent to itself. |
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get_ascii(self,
show_internal=True,
compact=False)
Returns a string containing an ascii drawing of the tree. |
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get_children(self)
Returns an independent list of node's children. |
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get_farthest_leaf(self,
topology_only=False)
Returns node's farthest descendant node (which is always a leaf), and the
distance to it. |
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get_leaf_names(self)
Returns the list of terminal node names under the current node. |
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get_leaves(self)
Returns the list of terminal nodes (leaves) under this node. |
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get_leaves_by_name(self,
name)
Returns a list of nodes marching a given name. |
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get_midpoint_outgroup(self)
Returns the node that divides the current tree into two
distance-balanced partitions. |
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get_sisters(self)
Returns an indepent list of sister nodes. |
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get_tree_root(self)
Returns the absolute root node of current tree structure. |
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iter_descendants(self,
strategy=' preorder ' )
Returns an iterator over descendant nodes. |
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iter_leaf_names(self)
Returns an iterator over the leaf names under this node. |
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iter_leaves(self)
Returns an iterator over the leaves under this node. |
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populate(self,
size,
names_library=[ ] ,
reuse_names=True)
Populates the partition under this node with a given number
of leaves. |
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prune(self,
nodes)
Prunes the topology of this node in order to conserve only a selected
list of leaf or internal nodes. |
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remove_child(self,
child)
Removes a child from this node (parent and child nodes still exit but
are no longer connected). |
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render(self,
file_name,
layout=None,
w=None,
h=None,
img_properties=None,
header=None)
Renders the tree structure into an image file. |
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show(self,
layout=None,
image_properties=None)
Begins an interative session to visualize this node structure. |
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swap_childs(self)
Swaps current childs order. |
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traverse(self,
strategy=' preorder ' )
Returns an iterator that traverse the tree structure under this node. |
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write(self,
features=None,
outfile=None,
format=0)
Returns the newick representation of this node
topology. |
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