Package Bio :: Package Phylo :: Module PhyloXML :: Class ProteinDomain
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Class ProteinDomain

source code

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

Represents an individual domain in a domain architecture.

The locations use 0-based indexing, as most Python objects including SeqFeature do, rather than the usual biological convention starting at 1. This means the start and end attributes can be used directly as slice indexes on Seq objects.

Instance Methods [hide private]
 
__init__(self, value, start, end, confidence=None, id=None)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
source code
 
to_seqfeature(self) source code

Inherited from BaseTree.TreeElement: __repr__, __str__

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

Class Methods [hide private]
 
from_seqfeature(cls, feat) source code
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, value, start, end, confidence=None, id=None)
(Constructor)

source code 
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Parameters:
  • start (non-negative integer) - start of the domain on the sequence, using 0-based indexing
  • end (non-negative integer) - end of the domain on the sequence
  • confidence (float) - can be used to store e.g. E-values
  • id (string) - unique identifier/name
Overrides: object.__init__
(inherited documentation)