def optimize_model(self, treefile, seqfile, extra="-m GTRGAMMA -n test"):
"""Optimizes the RAxML model"""
# initialize parameters based on input
cmd = "raxmlHPC -t %s -s %s %s" %\
(treefile, seqfile, extra)
raxml.init_program(self.adef, self.tr, cmd.split(' '))
# optimize
raxml.optimize_model(self.adef, self.tr)
# reset best LH
if self.best_vector is not None:
raxml.delete_best_vector(self.best_vector)
self.best_vector, self.best_LH, self.weight_sum = raxml.compute_best_LH(self.tr)
# set flags
self.optimal = True
def __del__(self):
raxml.delete_analdef(self.adef)
raxml.delete_tree(self.tr)
if self.best_vector is not None:
raxml.delete_best_vector(self.best_vector)
