def _bring_orgs_to_desired_number_in_tree(tree, mutation_rate,
delta_number_of_orgs):
"""
Adds (by fitness) or removes (uniformily) orgs from tree by delta number
of orgs (positive adds, negative removes).
Returns modified tree
"""
while delta_number_of_orgs > 0:
tree = _add_child_by_fitness_to_tree(tree, mutation_rate)
delta_number_of_orgs -= 1
while delta_number_of_orgs < 0:
tree, removed_org = fitness_tree.remove_leaf_uniformly(tree)
delta_number_of_orgs += 1
return tree
def _bring_orgs_to_desired_number_in_tree(tree, mutation_rate,
delta_number_of_orgs):
"""
Adds (by fitness) or removes (uniformily) orgs from tree by delta number
of orgs (positive adds, negative removes).
Returns modified tree
"""
while delta_number_of_orgs > 0:
tree = _add_child_by_fitness_to_tree(tree, mutation_rate)
delta_number_of_orgs -= 1
while delta_number_of_orgs < 0:
tree, removed_org = fitness_tree.remove_leaf_uniformly(tree)
delta_number_of_orgs += 1
return tree
def moran_death_birth(orgs, mutation_rate, desired_number_of_orgs=None):
"""
Method to execute the replacement of organism in a death-birth
fashion using fecundity to replace the randomly selected death organism
"""
tree = fitness_tree.build_tree(orgs)
if desired_number_of_orgs is None:
desired_number_of_orgs = len(orgs)
tree = _bring_orgs_to_desired_number_in_tree(
tree, mutation_rate, desired_number_of_orgs - len(orgs))
for _ in range(desired_number_of_orgs):
tree, removed_org = fitness_tree.remove_leaf_uniformly(tree)
tree = _add_child_by_fitness_to_tree(tree, mutation_rate)
return fitness_tree.tree_to_list(tree)
def moran_death_birth(orgs, mutation_rate, desired_number_of_orgs=None):
"""
Method to execute the replacement of organism in a death-birth
fashion using fecundity to replace the randomly selected death organism
"""
tree = fitness_tree.build_tree(orgs)
if desired_number_of_orgs is None:
desired_number_of_orgs = len(orgs)
tree = _bring_orgs_to_desired_number_in_tree(
tree, mutation_rate, desired_number_of_orgs - len(orgs))
for _ in range(desired_number_of_orgs):
tree, removed_org = fitness_tree.remove_leaf_uniformly(tree)
tree = _add_child_by_fitness_to_tree(tree, mutation_rate)
return fitness_tree.tree_to_list(tree)