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

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          object --+        
BaseTree.TreeElement --+    
            PhyloElement --+

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)
Initialize the class.
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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)

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Initialize the class.
  • 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__

Class Variable Details [hide private]