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Package Bio :: Package Phylo :: Module PhyloXML :: Class Annotation
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Class Annotation

source code

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

The annotation of a molecular sequence.

It is recommended to annotate by using the optional 'ref' attribute (some examples of acceptable values for the ref attribute: 'GO:0008270', 'KEGG:Tetrachloroethene degradation', 'EC:1.1.1.1').

Instance Methods [hide private]
 
__init__(self, ref=None, source=None, evidence=None, type=None, desc=None, confidence=None, uri=None, properties=None)
x.__init__(...) initializes x; see help(type(x)) for signature		 source code

Inherited from BaseTree.TreeElement: __repr__, __str__

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

Class Variables [hide private]
  re_ref = re.compile(r'[a-zA-Z0-9_]+:[a-zA-Z0-9_\.-\s]+')
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, ref=None, source=None, evidence=None, type=None, desc=None, confidence=None, uri=None, properties=None)
(Constructor)

source code 

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:
  • source - plain-text source for this annotation
  • evidence - describe evidence as free text (e.g. 'experimental')
  • desc - free text description
  • confidence - state the type and value of support (type Confidence)
  • properties - list of typed and referenced annotations from external resources
Overrides: object.__init__
(inherited documentation)

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