Container base class for both clear and possible orthologs. More...

Inheritance diagram for cls.HSGeneOrthologyMapping.CMappingContainerBase:

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Collaboration diagram for cls.HSGeneOrthologyMapping.CMappingContainerBase:

Public Member Functions
def	__init__ (s, paths)
	Constructor. More...

def	Convert (s, key, isHS=True, incPossible=False)
	Convert genes to their orthologs. More...

Public Member Functions inherited from cls.PairwiseMapperBase.CPairwiseMapperBase
def	GetPaths (s)
	Get CPaths object stored here. More...

Static Public Attributes
	GenuineClass = None;
	Class name for well defined orthologs, according to Ensembl. More...

Detailed Description

Container base class for both clear and possible orthologs.

Ensembl has a two way classification of orthologs. One are defined as
clear orthologs, but others are putative, termed 'possible'. The mechanism
to read them is the same.

We derive from cls.PairwiseMapperBase.CPairwiseMapperBase as we want to
complications arising from more specialized classes.

Constructor & Destructor Documentation

◆ init()

def cls.HSGeneOrthologyMapping.CMappingContainerBase.__init__	(	s,
		paths
	)

Constructor.

    @param paths  CPaths object.

Reimplemented from cls.PairwiseMapperBase.CPairwiseMapperBase.

Member Function Documentation

◆ Convert()

def cls.HSGeneOrthologyMapping.CMappingContainerBase.Convert	(	s,
		key,
		isHS = `True`,
		incPossible = `False`
	)

Convert genes to their orthologs.

    Parameters are the same as in CHSGeneOrthologyMappingBase.Convert.
    @param incPossible  Also include the set of putative/possible
     orthologs.

Member Data Documentation

◆ GenuineClass

cls.HSGeneOrthologyMapping.CMappingContainerBase.GenuineClass = None;

static

Class name for well defined orthologs, according to Ensembl.

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

cls/HSGeneOrthologyMapping.py

Public Member Functions

Static Public Attributes