Package Bio :: Package Phylo :: Module PhyloXML :: Class SequenceRelation
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Class SequenceRelation

source code

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

Express a typed relationship between two sequences.

For example, this could be used to describe an orthology (in which case attribute 'type' is 'orthology').

Instance Methods [hide private]
 
__init__(self, type, id_ref_0, id_ref_1, distance=None, confidence=None)
x.__init__(...) initializes x; see x.__class__.__doc__ 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]
  ok_type = set(['one_to_one_orthology', 'orthology', 'other', '...
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, type, id_ref_0, id_ref_1, distance=None, confidence=None)
(Constructor)

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

Parameters:
  • id_ref_0 (Id) - first sequence reference identifier
  • id_ref_1 (Id) - second sequence reference identifier
  • distance (float) - distance between the two sequences
  • type (restricted string) - describe the type of relationship
  • confidence (Confidence) - confidence value for this relation
Overrides: object.__init__
(inherited documentation)

Class Variable Details [hide private]

ok_type

Value:
set(['one_to_one_orthology',
     'orthology',
     'other',
     'paralogy',
     'super_orthology',
     'ultra_paralogy',
     'unknown',
     'xenology'])