Bio.Nexus.Nodes module¶
Linked list functionality for use in Bio.Nexus.
Provides functionality of a linked list. Each node has one (or none) predecessor, and an arbitrary number of successors. Nodes can store arbitrary data in a NodeData class.
Subclassed by Nexus.Trees to store phylogenetic trees.
Bug reports to Frank Kauff (fkauff@biologie.uni-kl.de)
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exception
Bio.Nexus.Nodes.
ChainException
¶ Bases:
Exception
Provision for the management of Chain exceptions.
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exception
Bio.Nexus.Nodes.
NodeException
¶ Bases:
Exception
Provision for the management of Node exceptions.
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class
Bio.Nexus.Nodes.
Chain
¶ Bases:
object
Stores a list of nodes that are linked together.
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__init__
(self)¶ Initialize a node chain.
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all_ids
(self)¶ Return a list of all node ids.
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add
(self, node, prev=None)¶ Attach node to another.
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collapse
(self, id)¶ Delete node from chain and relinks successors to predecessor.
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kill
(self, id)¶ Kill a node from chain without caring to what it is connected.
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unlink
(self, id)¶ Disconnect node from his predecessor.
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link
(self, parent, child)¶ Connect son to parent.
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is_parent_of
(self, parent, grandchild)¶ Check if grandchild is a subnode of parent.
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trace
(self, start, finish)¶ Return a list of all node_ids between two nodes (excluding start, including end).
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class
Bio.Nexus.Nodes.
Node
(data=None)¶ Bases:
object
A single node.
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__init__
(self, data=None)¶ Represent a node with one predecessor and multiple successors.
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set_id
(self, id)¶ Set the id of a node, if not set yet.
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get_id
(self)¶ Return the node’s id.
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get_succ
(self)¶ Return a list of the node’s successors.
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get_prev
(self)¶ Return the id of the node’s predecessor.
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add_succ
(self, id)¶ Add a node id to the node’s successors.
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remove_succ
(self, id)¶ Remove a node id from the node’s successors.
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set_succ
(self, new_succ)¶ Set the node’s successors.
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set_prev
(self, id)¶ Set the node’s predecessor.
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get_data
(self)¶ Return a node’s data.
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set_data
(self, data)¶ Set a node’s data.
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