def find_perfectly_conserved_sites(self,edges=None):
"""
See subclass_sitealignment.BasalSiteAlignmentFunctions.find_perfectly_conserved_sites
"""
return BasalSiteAlignmentFunctions.find_perfectly_conserved_sites(
self,edges=edges
)
def align_all_sites(self,edges=None,minimal_edges=2):
"""
See subclass_sitealignment.BasalSiteAlignmentFunctions.align_all_sites
"""
return BasalSiteAlignmentFunctions.align_all_sites(
self,edges=edges,
minimal_edges=minimal_edges
)
def find_fully_connected_subgraphs(self,edges=None,max_missing_edges=2):
"""
See subclass_sitealignment.BasalSiteAlignmentFunctions.find_fully_connected_subgraphs
"""
return BasalSiteAlignmentFunctions.find_fully_connected_subgraphs(
self,edges=edges,
max_missing_edges=max_missing_edges
)
def find_conserved_sites(self,edges=None):
"""
See subclass_sitealignment.BasalSiteAlignmentFunctions.find_conserved_sites
"""
# if edges is not applied get by definition form the OrganismGraph
if not edges: edges = self.organism_set_size() - 1
return BasalSiteAlignmentFunctions.find_conserved_sites(
self,edges=edges
)
