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src/c/o/cogent-1.5.3/tests/test_maths/test_unifrac/test_fast_tree.py   cogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.parse.tree import DndParser
from cogent.maths.unifrac.fast_tree import (count_envs, sum_env_dict, 
    index_envs, get_branch_lengths, index_tree, bind_to_array, 
    bind_to_parent_array, _is_parent_empty, delete_empty_parents,
        a[3] = [1,0,0]
        a[6] = [0,0,1]
        sum_descendants(bindings)
        self.assertEqual(a, \
            array([[0,1,0],[0,1,0],[0,1,0],[1,0,0],[0,3,0],[1,0,0],\
        envs = self.count_array
        bound_indices = bind_to_array(self.nodes, envs)
        sum_descendants(bound_indices)
        bl = self.branch_lengths
        tip_indices = [n._leaf_index for n in self.t.tips()]
        envs = self.count_array
        bound_indices = bind_to_array(self.nodes, envs)
        sum_descendants(bound_indices)
        bl = self.branch_lengths
        tip_indices = [n._leaf_index for n in self.t.tips()]
    def test_weighted_unifrac_vector(self):
        """weighted_unifrac_vector should ret correct results for model tree"""
        envs = self.count_array
        bound_indices = bind_to_array(self.nodes, envs)
        sum_descendants(bound_indices)

src/p/y/pycogent-HEAD/tests/test_maths/test_unifrac/test_fast_tree.py   pycogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.parse.tree import DndParser
from cogent.maths.unifrac.fast_tree import (count_envs, sum_env_dict, 
    index_envs, get_branch_lengths, index_tree, bind_to_array, 
    bind_to_parent_array, _is_parent_empty, delete_empty_parents,
        a[3] = [1,0,0]
        a[6] = [0,0,1]
        sum_descendants(bindings)
        self.assertEqual(a, \
            array([[0,1,0],[0,1,0],[0,1,0],[1,0,0],[0,3,0],[1,0,0],\
        envs = self.count_array
        bound_indices = bind_to_array(self.nodes, envs)
        sum_descendants(bound_indices)
        bl = self.branch_lengths
        tip_indices = [n._leaf_index for n in self.t.tips()]
        envs = self.count_array
        bound_indices = bind_to_array(self.nodes, envs)
        sum_descendants(bound_indices)
        bl = self.branch_lengths
        tip_indices = [n._leaf_index for n in self.t.tips()]
    def test_weighted_unifrac_vector(self):
        """weighted_unifrac_vector should ret correct results for model tree"""
        envs = self.count_array
        bound_indices = bind_to_array(self.nodes, envs)
        sum_descendants(bound_indices)