Bio.Phylo.PhyloXML.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.

Instance Methods

__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__

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

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

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)