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python-biopython  1.60
Public Member Functions | Public Attributes | Static Public Attributes
Bio.Phylo.PhyloXML.SequenceRelation Class Reference
Inheritance diagram for Bio.Phylo.PhyloXML.SequenceRelation:
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List of all members.

Public Member Functions

def __init__
def __repr__

Public Attributes

 distance
 type
 id_ref_0
 id_ref_1
 confidence

Static Public Attributes

tuple ok_type

Detailed Description

Express a typed relationship between two sequences.

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

: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

Definition at line 1173 of file PhyloXML.py.


Constructor & Destructor Documentation

def Bio.Phylo.PhyloXML.SequenceRelation.__init__ (   self,
  type,
  id_ref_0,
  id_ref_1,
  distance = None,
  confidence = None 
)

Definition at line 1195 of file PhyloXML.py.

01195 
01196             distance=None, confidence=None):
01197         _check_str(type, self.ok_type.__contains__)
01198         self.distance = distance
01199         self.type = type
01200         self.id_ref_0 = id_ref_0
01201         self.id_ref_1 = id_ref_1
01202         self.confidence = confidence
01203 

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Member Function Documentation

def Bio.Phylo.BaseTree.TreeElement.__repr__ (   self) [inherited]
Show this object's constructor with its primitive arguments.

Definition at line 216 of file BaseTree.py.

00216 
00217     def __repr__(self):
00218         """Show this object's constructor with its primitive arguments."""
00219         def pair_as_kwarg_string(key, val):
00220             if isinstance(val, basestring):
00221                 return "%s='%s'" % (key, _sugar.trim_str(unicode(val)))
00222             return "%s=%s" % (key, val)
00223         return u'%s(%s)' % (self.__class__.__name__,
00224                             ', '.join(pair_as_kwarg_string(key, val)
00225                                   for key, val in self.__dict__.iteritems()
00226                                   if val is not None and
00227                                   type(val) in (str, int, float, bool, unicode)
00228                                   ))


Member Data Documentation

Definition at line 1201 of file PhyloXML.py.

Definition at line 1197 of file PhyloXML.py.

Definition at line 1199 of file PhyloXML.py.

Definition at line 1200 of file PhyloXML.py.

Initial value:
set(('orthology', 'one_to_one_orthology', 'super_orthology',
        'paralogy', 'ultra_paralogy', 'xenology', 'unknown', 'other'))

Definition at line 1191 of file PhyloXML.py.

Definition at line 1198 of file PhyloXML.py.


The documentation for this class was generated from the following file: