def __connection_in_extra_genes_step_1(self, control, connected_nodes):
"""
calculate c[1]: whether 'extra-gene' is directly connected to the LGN
connected_nodes = list[set()] ==> remember to 'flatten' them first
"""
# use set() since we do not pay attention to how many times
# extra genes connect with LGN
nodes = set(helper.list_of_sets_to_list(connected_nodes))
for gene in nodes:
if gene in control:
control[gene][1] += 1
else:
# In the same block, this thing should never happen!!!
print "Problem!!! internal validation 1"
return control
def __connection_in_extra_genes_step_2(self, control, connected_nodes):
"""
calculate c[2] ... c[n+1]: number of times it's connected to SLGN(0), ...,
whether 'extra-gene' is connected to SLGN(i), ... ,
whether 'extra-gene' is connected to SLGN(n-1))
connected_nodes_in_subLGN = list[]
"""
number_of_LGN_genes = len(self.genes_in_lgn)
list_of_connected_nodes = helper.list_of_sets_to_list(connected_nodes)
calculated_node = set()
set_of_connected_nodes = set(list_of_connected_nodes)
for (index, set_of_genes) in enumerate(connected_nodes):
for gene in set_of_genes:
if gene in control:
for k in range(0, number_of_LGN_genes):
control[gene][k + 2] = 1
if gene not in calculated_node:
control[gene][index + 2] = 0
else:
# In the same block, this thing should never happen!!!
print "Problem!!! internal validation 2"
return control
