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

Class Annotation

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

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

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 x.__class__.__doc__ for signature

source code

Inherited from BaseTree.TreeElement: __repr__, __str__

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

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 x.__class__.__doc__ for signature

Overrides: object.__init__: (inherited documentation)

Class Annotation

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

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