treetime/treetime.py
def _set_branch_length_mode(self, branch_length_mode):
        '''
        if branch_length mode is not explicitly set, set according to
        empirical branch length distribution in input tree

        Parameters
        ----------

         branch_length_mode : str, 'input', 'joint', 'marginal'
            if the maximal branch length in the tree is longer than 0.05, this will
            default to 'input'. Otherwise set to 'joint'
        '''
        if branch_length_mode in ['joint', 'marginal', 'input']:
            self.branch_length_mode = branch_length_mode
        elif self.aln:
            bl_dis = [n.branch_length for n in self.tree.find_clades() if n.up]
            max_bl = np.max(bl_dis)
            if max_bl>0.1:
                bl_mode = 'input'
            else:
                bl_mode = 'joint'
            self.logger("TreeTime._set_branch_length_mode: maximum branch length is %1.3e, using branch length mode %s"%(max_bl, bl_mode),1)
            self.branch_length_mode = bl_mode
        else:
            self.branch_length_mode = 'input'
def _set_branch_length_mode(self, branch_length_mode):
        '''
        if branch_length mode is not explicitly set, set according to
        empirical branch length distribution in input tree

        Parameters
        ----------

         branch_length_mode : str, 'input', 'joint', 'marginal'
            if the maximal branch length in the tree is longer than 0.05, this will
            default to 'input'. Otherwise set to 'joint'
        '''
        if branch_length_mode in ['joint', 'marginal', 'input']:
            self.branch_length_mode = branch_length_mode
        elif self.aln:
            bl_dis = [n.branch_length for n in self.tree.find_clades() if n.up]
            max_bl = np.max(bl_dis)
            if max_bl>0.1:
                bl_mode = 'input'
            else:
                bl_mode = 'joint'
            self.logger("TreeTime._set_branch_length_mode: maximum branch length is %1.3e, using branch length mode %s"%(max_bl, bl_mode),1)
            self.branch_length_mode = bl_mode
        else:
            self.branch_length_mode = 'input'
if branch_length mode is not explicitly set, set according to
        empirical branch length distribution in input tree

        Parameters
        ----------

         branch_length_mode : str, 'input', 'joint', 'marginal'
            if the maximal branch length in the tree is longer than 0.05, this will
            default to 'input'. Otherwise set to 'joint'