treetime/clock_tree.py
def _set_precision(self, precision):
        '''
        function that sets precision to an (hopfully) reasonable guess based
        on the length of the sequence if not explicitly set
        '''
        # if precision is explicitly specified, use it.

        if self.one_mutation:
            self.min_width = 10*self.one_mutation
        else:
            self.min_width = 0.001
        if precision in [0,1,2,3]:
            self.precision=precision
            if self.one_mutation and self.one_mutation<1e-4 and precision<2:
                self.logger("ClockTree._set_precision: FOR LONG SEQUENCES (>1e4) precision>=2 IS RECOMMENDED."
                            " \n\t **** precision %d was specified by the user"%precision, level=0)
        else:
            # otherwise adjust it depending on the minimal sensible branch length
            if self.one_mutation:
                if self.one_mutation>1e-4:
                    self.precision=1
                else:
                    self.precision=2
            else:
                self.precision=1
            self.logger("ClockTree: Setting precision to level %s"%self.precision, 2)

        if self.precision==0:
            self.node_grid_points = ttconf.NODE_GRID_SIZE_ROUGH
            self.branch_grid_points = ttconf.BRANCH_GRID_SIZE_ROUGH
            self.n_integral = ttconf.N_INTEGRAL_ROUGH
        elif self.precision==2:
            self.node_grid_points = ttconf.NODE_GRID_SIZE_FINE
            self.branch_grid_points = ttconf.BRANCH_GRID_SIZE_FINE
            self.n_integral = ttconf.N_INTEGRAL_FINE
        elif self.precision==3:
            self.node_grid_points = ttconf.NODE_GRID_SIZE_ULTRA
            self.branch_grid_points = ttconf.BRANCH_GRID_SIZE_ULTRA
            self.n_integral = ttconf.N_INTEGRAL_ULTRA
        else:
            self.node_grid_points = ttconf.NODE_GRID_SIZE
            self.branch_grid_points = ttconf.BRANCH_GRID_SIZE
            self.n_integral = ttconf.N_INTEGRAL
def _set_precision(self, precision):
        '''
        function that sets precision to an (hopfully) reasonable guess based
        on the length of the sequence if not explicitly set
        '''
        # if precision is explicitly specified, use it.

        if self.one_mutation:
            self.min_width = 10*self.one_mutation
        else:
            self.min_width = 0.001
        if precision in [0,1,2,3]:
            self.precision=precision
            if self.one_mutation and self.one_mutation<1e-4 and precision<2:
                self.logger("ClockTree._set_precision: FOR LONG SEQUENCES (>1e4) precision>=2 IS RECOMMENDED."
                            " \n\t **** precision %d was specified by the user"%precision, level=0)
        else:
            # otherwise adjust it depending on the minimal sensible branch length
            if self.one_mutation:
                if self.one_mutation>1e-4:
                    self.precision=1
                else:
                    self.precision=2
            else:
                self.precision=1
            self.logger("ClockTree: Setting precision to level %s"%self.precision, 2)

        if self.precision==0:
            self.node_grid_points = ttconf.NODE_GRID_SIZE_ROUGH
            self.branch_grid_points = ttconf.BRANCH_GRID_SIZE_ROUGH
            self.n_integral = ttconf.N_INTEGRAL_ROUGH
        elif self.precision==2:
            self.node_grid_points = ttconf.NODE_GRID_SIZE_FINE
            self.branch_grid_points = ttconf.BRANCH_GRID_SIZE_FINE
            self.n_integral = ttconf.N_INTEGRAL_FINE
        elif self.precision==3:
            self.node_grid_points = ttconf.NODE_GRID_SIZE_ULTRA
            self.branch_grid_points = ttconf.BRANCH_GRID_SIZE_ULTRA
            self.n_integral = ttconf.N_INTEGRAL_ULTRA
        else:
            self.node_grid_points = ttconf.NODE_GRID_SIZE
            self.branch_grid_points = ttconf.BRANCH_GRID_SIZE
            self.n_integral = ttconf.N_INTEGRAL
def _set_precision ( self , precision ) : # if precision is explicitly specified, use it. if self . one_mutation : self . min_width = 10 * self . one_mutation else : self . min_width = 0.001 if precision in [ 0 , 1 , 2 , 3 ] : self . precision = precision if self . one_mutation and self . one_mutation < 1e-4 and precision < 2 : self . logger ( "ClockTree._set_precision: FOR LONG SEQUENCES (>1e4) precision>=2 IS RECOMMENDED." " \n\t **** precision %d was specified by the user" % precision , level = 0 ) else : # otherwise adjust it depending on the minimal sensible branch length if self . one_mutation : if self . one_mutation > 1e-4 : self . precision = 1 else : self . precision = 2 else : self . precision = 1 self . logger ( "ClockTree: Setting precision to level %s" % self . precision , 2 ) if self . precision == 0 : self . node_grid_points = ttconf . NODE_GRID_SIZE_ROUGH self . branch_grid_points = ttconf . BRANCH_GRID_SIZE_ROUGH self . n_integral = ttconf . N_INTEGRAL_ROUGH elif self . precision == 2 : self . node_grid_points = ttconf . NODE_GRID_SIZE_FINE self . branch_grid_points = ttconf . BRANCH_GRID_SIZE_FINE self . n_integral = ttconf . N_INTEGRAL_FINE elif self . precision == 3 : self . node_grid_points = ttconf . NODE_GRID_SIZE_ULTRA self . branch_grid_points = ttconf . BRANCH_GRID_SIZE_ULTRA self . n_integral = ttconf . N_INTEGRAL_ULTRA else : self . node_grid_points = ttconf . NODE_GRID_SIZE self . branch_grid_points = ttconf . BRANCH_GRID_SIZE self . n_integral = ttconf . N_INTEGRAL
function that sets precision to an (hopfully) reasonable guess based
        on the length of the sequence if not explicitly set
function that sets precision to an ( hopfully ) reasonable guess based on the length of the sequence if not explicitly set