def create_ilp_formulation_for_restricted_median(cfg):
try:
model = gurobipy.Model(cfg.name_model)
logger.info("START CREATING MODEL.")
dot_rs = model.addVars(
{x
for x, cond in cfg.allowable_telomers.items() if cond},
vtype=gurobipy.GRB.BINARY)
rs = define_matching_vars(model=model,
edge_set=cfg.allowable_ancestral_edges,
edge_conditions=cfg.connection_constrs,
vertex_set=dot_rs,
vertex_conditions=cfg.allowable_telomers,
name="rs")
tilde_bs, hat_bs = [], []
for i in range(cfg.number_of_genomes):
tilde_b, hat_b = di_dist_without_singletons(model=model,
rs=rs,
cfg=cfg,
ind=i)
tilde_bs.append(tilde_b)
hat_bs.append(hat_b)
logger.info("CREATING BIG CONSTRAINT")
model.addConstr(tilde_bs[0].sum('*') + tilde_bs[1].sum('*') -
dot_rs.sum('*') - hat_bs[0].sum('*') -
hat_bs[1].sum('*') == len(cfg.ind_ancestral_set) // 2 +
cfg.number_of_cycles + cfg.number_of_even_paths // 2)
logger.info("CREATING OBJECTIVE FUNCTION.")
model.setObjective(
tilde_bs[2].sum('*') - 0.5 * dot_rs.sum('*') - hat_bs[2].sum('*'),
gurobipy.GRB.MAXIMIZE)
logger.info("FINISH CREATE MODEL.")
model.params.logFile = cfg.log_file
model.params.MIPFocus = 2
model.params.timeLimit = cfg.time_limit
model.optimize()
logger.info("The number of cycles and paths is " +
str(int(model.objVal)))
answer = get_param_of_solution_for_restricted_median(model=model,
cfg=cfg,
rs=rs,
dot_rs=dot_rs)
return answer
except gurobipy.GurobiError as e:
logger.error(
"Some error has been raised. Please, report to github bug tracker. \n Text exception: {0}"
.format(e))
def create_ilp_formulation_for_halvings_without_singletons(cfg):
try:
model = gurobipy.Model(cfg.name_model)
logger.info("START CREATING MODEL.")
dot_rs = model.addVars(
{
x
for x, cond in cfg.allowable_ancestral_telomers.items() if cond
},
vtype=gurobipy.GRB.BINARY)
rs = define_matching_vars(
model=model,
edge_set=cfg.allowable_ancestral_edges,
edge_conditions=cfg.connection_ancestral_constrs,
vertex_set=dot_rs,
vertex_conditions=cfg.allowable_ancestral_telomers,
name="rs")
tilde_b, hat_b = di_dist_without_singletons(model=model,
rs=rs,
cfg=cfg,
ind=0)
tilde_a, hat_a = ddi_dist_without_singletons(model=model,
rs=rs,
cfg=cfg)
logger.info("CREATING OBJECTIVE FUNCTION.")
model.setObjective(
tilde_b.sum('*') + tilde_a.sum('*') - 1.5 * dot_rs.sum('*') -
hat_b.sum('*') - hat_a.sum('*'), gurobipy.GRB.MAXIMIZE)
logger.info("FINISH CREATE MODEL.")
model.params.logFile = cfg.log_file
model.params.MIPFocus = 2
model.params.timeLimit = cfg.time_limit
model.optimize()
logger.info("The number of cycles and paths is " +
str(int(model.objVal)))
answer = get_param_of_solution_for_halving_problem(model=model,
cfg=cfg,
rs=rs,
dot_rs=dot_rs)
return answer
except gurobipy.GurobiError as e:
logger.error(
"Some error has been raised. Please, report to github bug tracker. \n Text exception: {0}"
.format(e))
return None