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python-biopython  1.60
Public Member Functions | Public Attributes | Static Public Attributes
Bio.Phylo.PhyloXML.Taxonomy Class Reference
Inheritance diagram for Bio.Phylo.PhyloXML.Taxonomy:
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Collaboration diagram for Bio.Phylo.PhyloXML.Taxonomy:
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List of all members.

Public Member Functions

def __init__
def __str__
def __repr__

Public Attributes

 id_source
 id
 code
 scientific_name
 authority
 rank
 uri
 common_names
 synonyms
 other

Static Public Attributes

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

Detailed Description

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

Definition at line 1204 of file PhyloXML.py.


Constructor & Destructor Documentation

def Bio.Phylo.PhyloXML.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 
)

Definition at line 1253 of file PhyloXML.py.

01253 
01254             ):
01255         _check_str(code, self.re_code.match)
01256         _check_str(rank, self.ok_rank.__contains__)
01257         self.id_source = id_source
01258         self.id = id
01259         self.code = code
01260         self.scientific_name = scientific_name
01261         self.authority = authority
01262         self.rank = rank
01263         self.uri = uri
01264         self.common_names = common_names or []
01265         self.synonyms = synonyms or []
01266         self.other = other or []

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Member Function Documentation

def Bio.Phylo.BaseTree.TreeElement.__repr__ (   self) [inherited]
Show this object's constructor with its primitive arguments.

Definition at line 216 of file BaseTree.py.

00216 
00217     def __repr__(self):
00218         """Show this object's constructor with its primitive arguments."""
00219         def pair_as_kwarg_string(key, val):
00220             if isinstance(val, basestring):
00221                 return "%s='%s'" % (key, _sugar.trim_str(unicode(val)))
00222             return "%s=%s" % (key, val)
00223         return u'%s(%s)' % (self.__class__.__name__,
00224                             ', '.join(pair_as_kwarg_string(key, val)
00225                                   for key, val in self.__dict__.iteritems()
00226                                   if val is not None and
00227                                   type(val) in (str, int, float, bool, unicode)
00228                                   ))

Show the class name and an identifying attribute.

Definition at line 1267 of file PhyloXML.py.

01267 
01268     def __str__(self):
01269         """Show the class name and an identifying attribute."""
01270         if self.code is not None:
01271             return self.code
01272         if self.scientific_name is not None:
01273             return self.scientific_name
01274         if self.rank is not None:
01275             return self.rank
01276         if self.id is not None:
01277             return str(self.id)
01278         return self.__class__.__name__
01279 


Member Data Documentation

Definition at line 1260 of file PhyloXML.py.

Definition at line 1258 of file PhyloXML.py.

Definition at line 1263 of file PhyloXML.py.

Definition at line 1257 of file PhyloXML.py.

Definition at line 1256 of file PhyloXML.py.

Initial value:
set(('domain', 'kingdom', 'subkingdom', 'branch', 'infrakingdom',
        'superphylum', 'phylum', 'subphylum', 'infraphylum', 'microphylum',
        'superdivision', 'division', 'subdivision', 'infradivision',
        'superclass', 'class', 'subclass', 'infraclass', 'superlegion',
        'legion', 'sublegion', 'infralegion', 'supercohort', 'cohort',
        'subcohort', 'infracohort', 'superorder', 'order', 'suborder',
        'superfamily', 'family', 'subfamily', 'supertribe', 'tribe', 'subtribe',
        'infratribe', 'genus', 'subgenus', 'superspecies', 'species',
        'subspecies', 'variety', 'subvariety', 'form', 'subform', 'cultivar',
        'unknown', 'other'))

Definition at line 1234 of file PhyloXML.py.

Definition at line 1265 of file PhyloXML.py.

Definition at line 1261 of file PhyloXML.py.

tuple Bio.Phylo.PhyloXML.Taxonomy.re_code = re.compile(r'[a-zA-Z0-9_]{2,10}') [static]

Definition at line 1233 of file PhyloXML.py.

Definition at line 1259 of file PhyloXML.py.

Definition at line 1264 of file PhyloXML.py.

Definition at line 1262 of file PhyloXML.py.


The documentation for this class was generated from the following file: