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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]
        changes = fitch_descendants(bindings)
        self.assertEqual(changes, 2)
        self.assertEqual(a, \
        ab_counts = count_array[:, 0:2]
        bindings = bind_to_array(nodes, ab_counts)
        changes = fitch_descendants(bindings, counter=FitchCounter)
        self.assertEqual(changes, 1)
        orig_result = ab_counts.copy()
        #check that the original Fitch counter gives the expected 
        #incorrect parsimony result
        changes = fitch_descendants(bindings, counter=FitchCounterDense)

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]
        changes = fitch_descendants(bindings)
        self.assertEqual(changes, 2)
        self.assertEqual(a, \
        ab_counts = count_array[:, 0:2]
        bindings = bind_to_array(nodes, ab_counts)
        changes = fitch_descendants(bindings, counter=FitchCounter)
        self.assertEqual(changes, 1)
        orig_result = ab_counts.copy()
        #check that the original Fitch counter gives the expected 
        #incorrect parsimony result
        changes = fitch_descendants(bindings, counter=FitchCounterDense)