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Base classes for Bio.Phylo objects.
All object representations for phylogenetic trees should derive from these base classes in order to use the common methods defined on them.
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TreeElement Base class for all Bio.Phylo classes. |
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TreeMixin Methods for Tree- and Clade-based classes. |
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Tree A phylogenetic tree, containing global info for the phylogeny. |
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Clade A recursively defined sub-tree. |
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__package__ =
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Match a node by specified attribute values. 'terminal' is a special case: True restricts the search to external (leaf) nodes, False restricts to internal nodes, and None allows all tree elements to be searched, including phyloXML annotations. Otherwise, for a tree element to match the specification (i.e. for the function produced by _attribute_matcher to return True when given a tree element), it must have each of the attributes specified by the keys and match each of the corresponding values -- think 'and', not 'or', for multiple keys. |
Retrieve a matcher function by passing an arbitrary object. i.e. passing a TreeElement such as a Node or Tree instance returns an identity matcher, passing a type such as the PhyloXML.Taxonomy class returns a class matcher, and passing a dictionary returns an attribute matcher. The resulting 'match' function returns True when given an object matching the specification (identity, type or attribute values), otherwise False. This is useful for writing functions that search the tree, and probably shouldn't be used directly by the end user. |
Merge target specifications with keyword arguments. Dispatch the components to the various matcher functions, then merge into a single boolean function. |
Convert [targets] or *targets arguments to a single iterable. This helps other functions work like the built-in functions `max` and `min`. |
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