AlifestdIplotxShimNumpy

class AlifestdIplotxShimNumpy

Numpy-backed iplotx TreeDataProvider for alife-standard data.

This class assumes contiguous ids (id == row index) and topologically sorted rows (ancestors appear before descendants).

Parameters

ancestor_idsnp.ndarray: Integer array of ancestor ids; roots satisfy ancestor_ids[i] == i.
namesnp.ndarray, optional: Per-node name strings.
branch_lengthsnp.ndarray, optional: Per-node branch lengths (edge from parent to this node).

__init__(ancestor_ids: ndarray, names: ndarray | None = None, branch_lengths: ndarray | None = None) → None[source]

Methods

__init__(ancestor_ids: ndarray, names: ndarray | None = None, branch_lengths: ndarray | None = None) → None[source]

static check_dependencies() → bool[source]

static get_branch_length(node: _AlifestdNode) → float | None[source]

get_children(node: _AlifestdNode) → Sequence[_AlifestdNode][source]

get_leaves(node: _AlifestdNode | None = None) → Sequence[_AlifestdNode][source]

get_root() → _AlifestdNode[source]

get_subtree(node: _AlifestdNode) → AlifestdIplotxShimNumpy[source]

is_rooted() → bool[source]

levelorder() → Iterable[_AlifestdNode][source]

postorder() → Iterable[_AlifestdNode][source]

preorder() → Iterable[_AlifestdNode][source]

static tree_type() → type[source]