DEPRECATED

def write_alf_params_(self):
        """ DEPRECATED """
        if not hasattr(self, 'alf_dirs'):
            self.make_alf_dirs()

        if not hasattr(self, 'class_trees'):
            self.generate_class_trees()

        alf_params = {}
        for k in range(self.num_classes):
            alfdir = self.alf_dirs[k + 1]
            tree = self.class_trees[k + 1]
            datatype = self.datatype
            name = 'class{0}'.format(k + 1)
            num_genes = self.class_list[k]
            seqlength = self.gene_length_min
            gene_length_kappa = self.gene_length_kappa
            gene_length_theta = self.gene_length_theta
            alf_obj = ALF(tree=tree,
                          datatype=datatype, num_genes=num_genes,
                          seqlength=seqlength, gene_length_kappa=gene_length_kappa,
                          gene_length_theta=gene_length_theta, name=name, tmpdir=alfdir)
            if datatype == 'protein':
                alf_obj.params.one_word_model('WAG')
            else:
                alf_obj.params.jc_model()
            alf_params[k + 1] = alf_obj

        self.alf_params = alf_params