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|
{# This template is specifically for skbio.tree.TreeNode. #}
{% extends "autosummary/class.rst" %}
{% block methods %}
.. rubric:: Tree IO
.. autosummary::
:toctree:
~{{ name }}.read
~{{ name }}.write
.. rubric:: Tree navigation
.. autosummary::
:toctree:
~{{ name }}.ancestors
~{{ name }}.has_children
~{{ name }}.is_root
~{{ name }}.is_tip
~{{ name }}.lca
~{{ name }}.neighbors
~{{ name }}.path
~{{ name }}.root
~{{ name }}.siblings
.. rubric:: Tree traversal
.. autosummary::
:toctree:
~{{ name }}.levelorder
~{{ name }}.non_tips
~{{ name }}.postorder
~{{ name }}.pre_and_postorder
~{{ name }}.preorder
~{{ name }}.tips
~{{ name }}.traverse
.. rubric:: Tree copying
.. autosummary::
:toctree:
~{{ name }}.copy
~{{ name }}.deepcopy
~{{ name }}.subtree
.. rubric:: Tree manipulation
.. autosummary::
:toctree:
~{{ name }}.append
~{{ name }}.bifurcate
~{{ name }}.extend
~{{ name }}.insert
~{{ name }}.pop
~{{ name }}.prune
~{{ name }}.remove
~{{ name }}.remove_by_func
~{{ name }}.remove_deleted
~{{ name }}.shear
~{{ name }}.shuffle
~{{ name }}.unpack
~{{ name }}.unpack_by_func
.. rubric:: Tree rerooting
.. autosummary::
:toctree:
~{{ name }}.root_at
~{{ name }}.root_at_midpoint
~{{ name }}.root_by_outgroup
~{{ name }}.unroot
~{{ name }}.unrooted_copy
~{{ name }}.unrooted_deepcopy
~{{ name }}.unrooted_move
.. rubric:: Tree searching
.. autosummary::
:toctree:
~{{ name }}.assign_ids
~{{ name }}.cache_attr
~{{ name }}.clear_caches
~{{ name }}.create_caches
~{{ name }}.has_caches
~{{ name }}.find
~{{ name }}.find_all
~{{ name }}.find_by_func
~{{ name }}.find_by_id
~{{ name }}.index_tree
.. rubric:: Tree analysis
.. autosummary::
:toctree:
~{{ name }}.bipart
~{{ name }}.biparts
~{{ name }}.cophenet
~{{ name }}.count
~{{ name }}.depth
~{{ name }}.distance
~{{ name }}.height
~{{ name }}.is_bifurcating
~{{ name }}.maxdist
~{{ name }}.observed_node_counts
~{{ name }}.subset
~{{ name }}.subsets
~{{ name }}.total_length
.. rubric:: Tree comparison
.. autosummary::
:toctree:
~{{ name }}.compare_biparts
~{{ name }}.compare_cophenet
~{{ name }}.compare_rfd
~{{ name }}.compare_subsets
~{{ name }}.compare_wrfd
.. rubric:: Tree visualization
.. autosummary::
:toctree:
~{{ name }}.ascii_art
.. rubric:: Format conversion
.. autosummary::
:toctree:
~{{ name }}.assign_supports
~{{ name }}.from_linkage_matrix
~{{ name }}.from_taxdump
~{{ name }}.from_taxonomy
~{{ name }}.to_array
~{{ name }}.to_taxonomy
{% endblock %}
|
