Package Bio :: Package Phylo :: Module NewickIO :: Class Parser

Class Parser

object --+
         |
        Parser

Parse a Newick tree given a file handle.

Based on the parser in `Bio.Nexus.Trees`.

Instance Methods

[hide private]

__init__(self, handle)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

source code

parse(self, values_are_confidence=False, rooted=False)
Parse the text stream this object was initialized with.

source code

_parse_tree(self, text, rooted)
Parses the text representation into an Tree object.

source code

_parse_subtree(self, text)
Parse ``(a,b,c...)[[[xx]:]yy]`` into subcomponents, recursively.

source code

_parse_tag(self, text)
Extract the data for a node from text.

source code

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Class Methods

[hide private]

from_string(cls, treetext)

source code

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, handle)
(Constructor)

source code

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__: (inherited documentation)

_parse_tag(self, text)

source code

Extract the data for a node from text.

:returns: Clade instance containing any available data

Class Parser

__init__(self, handle) (Constructor)

_parse_tag(self, text)

init(self, handle)
(Constructor)