Package Bio :: Package Phylo :: Module PhyloXML :: Class Taxonomy

Class Taxonomy

          object --+        
                   |        
BaseTree.TreeElement --+    
                       |    
            PhyloElement --+
                           |
                          Taxonomy

Describe taxonomic information for a clade.

:Parameters:
    id_source : Id
        link other elements to a taxonomy (on the XML level)
    id : Id
        unique identifier of a taxon, e.g. Id('6500',
        provider='ncbi_taxonomy') for the California sea hare
    code : restricted string
        store UniProt/Swiss-Prot style organism codes, e.g. 'APLCA' for the
        California sea hare 'Aplysia californica'
    scientific_name : string
        the standard scientific name for this organism, e.g. 'Aplysia
        californica' for the California sea hare
    authority : string
        keep the authority, such as 'J. G. Cooper, 1863', associated with
        the 'scientific_name'
    common_names : list of strings
        common names for this organism
    synonyms : list of strings
        synonyms for this taxon?
    rank : restricted string
        taxonomic rank
    uri : Uri
        link
    other : list of Other objects
        non-phyloXML elements

Instance Methods

[hide private]

__init__(self, id_source=None, id=None, code=None, scientific_name=None, authority=None, rank=None, uri=None, common_names=None, synonyms=None, other=None)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

source code

__str__(self)
Show the class name and an identifying attribute.

source code

Inherited from BaseTree.TreeElement: __repr__

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

Class Variables

[hide private]

re_code = re.compile(r'[a-zA-Z0-9_]{2,10}')

ok_rank = set(['branch', 'class', 'cohort', 'cultivar', 'divis...

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, id_source=None, id=None, code=None, scientific_name=None, authority=None, rank=None, uri=None, common_names=None, synonyms=None, other=None)
(Constructor)

source code

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

Overrides: object.__init__: (inherited documentation)

str(self)
(Informal representation operator)

source code

Show the class name and an identifying attribute.

Overrides: object.__str__

Class Variable Details

[hide private]

ok_rank

Value:

set(['branch',
     'class',
     'cohort',
     'cultivar',
     'division',
     'domain',
     'family',
     'form',
...

Class Taxonomy

__init__(self, id_source=None, id=None, code=None, scientific_name=None, authority=None, rank=None, uri=None, common_names=None, synonyms=None, other=None) (Constructor)

__str__(self) (Informal representation operator)

ok_rank

init(self, id_source=None, id=None, code=None, scientific_name=None, authority=None, rank=None, uri=None, common_names=None, synonyms=None, other=None)
(Constructor)

str(self)
(Informal representation operator)