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 )