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

Public Member Functions

def __init__
def __repr__

Public Attributes

 ref
 source
 evidence
 type
 desc
 confidence
 uri
 properties

Static Public Attributes

tuple re_ref = re.compile(r'[a-zA-Z0-9_]+:[a-zA-Z0-9_\.\-\s]+')

Detailed Description

The annotation of a molecular sequence.

It is recommended to annotate by using the optional 'ref' attribute.

:Parameters:
    ref : string
        reference string, e.g. 'GO:0008270',
        'KEGG:Tetrachloroethene degradation', 'EC:1.1.1.1'
    source : string
        plain-text source for this annotation
    evidence : str
        describe evidence as free text (e.g. 'experimental')
    desc : string
        free text description
    confidence : Confidence
        state the type and value of support (type Confidence)
    properties : list
        typed and referenced annotations from external resources
    uri : Uri
        link

Definition at line 448 of file PhyloXML.py.


Constructor & Destructor Documentation

def Bio.Phylo.PhyloXML.Annotation.__init__ (   self,
  ref = None,
  source = None,
  evidence = None,
  type = None,
  desc = None,
  confidence = None,
  uri = None,
  properties = None 
)

Definition at line 478 of file PhyloXML.py.

00478 
00479             properties=None):
00480         _check_str(ref, self.re_ref.match)
00481         self.ref = ref
00482         self.source = source
00483         self.evidence = evidence
00484         self.type = type
00485         self.desc = desc
00486         self.confidence = confidence
00487         self.uri = uri
00488         self.properties = properties or []
00489 

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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                                   ))


Member Data Documentation

Definition at line 485 of file PhyloXML.py.

Definition at line 484 of file PhyloXML.py.

Definition at line 482 of file PhyloXML.py.

Definition at line 487 of file PhyloXML.py.

tuple Bio.Phylo.PhyloXML.Annotation.re_ref = re.compile(r'[a-zA-Z0-9_]+:[a-zA-Z0-9_\.\-\s]+') [static]

Definition at line 470 of file PhyloXML.py.

Definition at line 480 of file PhyloXML.py.

Definition at line 481 of file PhyloXML.py.

Definition at line 483 of file PhyloXML.py.

Definition at line 486 of file PhyloXML.py.


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