# Copyright (C) 2013 by Yanbo Ye (yeyanbo289@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.

"""Unit tests for the Bio.Phylo.Consensus module."""

import os
import unittest
import tempfile

# from io import StringIO
from Bio import Align
from Bio import AlignIO
from Bio import Phylo
from Bio.Phylo import BaseTree
from Bio.Phylo.TreeConstruction import DistanceCalculator
from Bio.Phylo.TreeConstruction import DistanceTreeConstructor
from Bio.Phylo import Consensus
from Bio.Phylo.Consensus import _BitString


temp_dir = tempfile.mkdtemp()


class BitStringTest(unittest.TestCase):
    """Test for _BitString class."""

    def test_bitstring(self):
        bitstr1 = _BitString("0011")
        bitstr2 = _BitString("0101")
        bitstr3 = _BitString("0001")
        bitstr4 = _BitString("0010")
        self.assertRaises(TypeError, _BitString, "10O1")
        self.assertEqual(bitstr1 & bitstr2, _BitString("0001"))
        self.assertEqual(bitstr1 | bitstr2, _BitString("0111"))
        self.assertEqual(bitstr1 ^ bitstr2, _BitString("0110"))
        self.assertFalse(bitstr1.contains(bitstr2))
        self.assertTrue(bitstr1.contains(bitstr1))
        self.assertTrue(bitstr1.contains(bitstr3))
        self.assertTrue(bitstr1.contains(bitstr4))
        self.assertFalse(bitstr1.independent(bitstr2))
        self.assertFalse(bitstr1.independent(bitstr4))
        self.assertTrue(bitstr2.independent(bitstr4))
        self.assertTrue(bitstr3.independent(bitstr4))
        self.assertFalse(bitstr1.iscompatible(bitstr2))
        self.assertTrue(bitstr1.iscompatible(bitstr3))
        self.assertTrue(bitstr1.iscompatible(bitstr4))
        self.assertTrue(bitstr2.iscompatible(bitstr4))
        self.assertTrue(bitstr3.iscompatible(bitstr4))


class ConsensusTest(unittest.TestCase):
    """Test for consensus methods."""

    def setUp(self):
        self.trees = list(Phylo.parse("./TreeConstruction/trees.tre", "newick"))

    def test_count_clades(self):
        bitstr_counts, len_trees = Consensus._count_clades(self.trees)
        self.assertEqual(len_trees, len(self.trees))
        self.assertEqual(len(bitstr_counts), 6)
        self.assertEqual(bitstr_counts[_BitString("11111")][0], 3)
        self.assertEqual(bitstr_counts[_BitString("11000")][0], 2)
        self.assertEqual(bitstr_counts[_BitString("00111")][0], 3)
        self.assertEqual(bitstr_counts[_BitString("00110")][0], 2)
        self.assertEqual(bitstr_counts[_BitString("00011")][0], 1)
        self.assertEqual(bitstr_counts[_BitString("01111")][0], 1)

    def test_strict_consensus(self):
        ref_trees = list(Phylo.parse("./TreeConstruction/strict_refs.tre", "newick"))
        # three trees
        consensus_tree = Consensus.strict_consensus(self.trees)
        # tree_file = StringIO()
        # Phylo.write(consensus_tree, tree_file, 'newick')
        self.assertTrue(Consensus._equal_topology(consensus_tree, ref_trees[0]))
        # tree 1 and tree 2
        consensus_tree = Consensus.strict_consensus(self.trees[:2])
        # tree_file = StringIO()
        # Phylo.write(consensus_tree, tree_file, 'newick')
        self.assertTrue(Consensus._equal_topology(consensus_tree, ref_trees[1]))
        # tree 1 and tree 3
        consensus_tree = Consensus.strict_consensus(self.trees[::2])
        # tree_file = StringIO()
        # Phylo.write(consensus_tree, tree_file, 'newick')
        self.assertTrue(Consensus._equal_topology(consensus_tree, ref_trees[2]))
        # tree_file.close()

    def test_majority_consensus(self):
        ref_trees = Phylo.parse("./TreeConstruction/majority_ref.tre", "newick")
        ref_tree = next(ref_trees)
        consensus_tree = Consensus.majority_consensus(self.trees)
        self.assertTrue(Consensus._equal_topology(consensus_tree, ref_tree))
        ref_tree = next(ref_trees)
        consensus_tree = Consensus.majority_consensus(self.trees, 1)
        self.assertTrue(Consensus._equal_topology(consensus_tree, ref_tree))

    def test_adam_consensus(self):
        ref_trees = list(Phylo.parse("./TreeConstruction/adam_refs.tre", "newick"))
        # three trees
        consensus_tree = Consensus.adam_consensus(self.trees)
        # tree_file = '/home/yeyanbo/adam.tres'
        # tree_file = StringIO()
        # Phylo.write(consensus_tree, tree_file, 'newick')
        self.assertTrue(Consensus._equal_topology(consensus_tree, ref_trees[0]))
        # tree 1 and tree 2
        consensus_tree = Consensus.adam_consensus(self.trees[:2])
        # tree_file = StringIO()
        # Phylo.write(consensus_tree, tree_file, 'newick')
        self.assertTrue(Consensus._equal_topology(consensus_tree, ref_trees[1]))
        # tree 1 and tree 3
        consensus_tree = Consensus.adam_consensus(self.trees[::2])
        # tree_file = StringIO()
        # Phylo.write(consensus_tree, tree_file, 'newick')
        self.assertTrue(Consensus._equal_topology(consensus_tree, ref_trees[2]))
        # tree_file.close()

    def test_get_support(self):
        support_tree = Consensus.get_support(self.trees[0], self.trees)
        clade = support_tree.common_ancestor(
            [support_tree.find_any(name="Beta"), support_tree.find_any(name="Gamma")]
        )
        self.assertEqual(clade.confidence, 2 * 100.0 / 3)
        clade = support_tree.common_ancestor(
            [support_tree.find_any(name="Alpha"), support_tree.find_any(name="Beta")]
        )
        self.assertEqual(clade.confidence, 3 * 100.0 / 3)
        clade = support_tree.common_ancestor(
            [support_tree.find_any(name="Delta"), support_tree.find_any(name="Epsilon")]
        )
        self.assertEqual(clade.confidence, 2 * 100.0 / 3)


class BootstrapTest(unittest.TestCase):
    """Test for bootstrap methods."""

    def setUp(self):
        self.msa = AlignIO.read("TreeConstruction/msa.phy", "phylip")
        self.alignment = Align.read("TreeConstruction/msa.phy", "phylip")

    def test_bootstrap(self):
        msa_list = list(Consensus.bootstrap(self.msa, 100))
        self.assertEqual(len(msa_list), 100)
        self.assertEqual(len(msa_list[0]), len(self.msa))
        self.assertEqual(len(msa_list[0][0]), len(self.msa[0]))

    def test_bootstrap_trees_msa(self):
        calculator = DistanceCalculator("blosum62")
        constructor = DistanceTreeConstructor(calculator)
        trees = list(Consensus.bootstrap_trees(self.msa, 100, constructor))
        self.assertEqual(len(trees), 100)
        self.assertIsInstance(trees[0], BaseTree.Tree)

    def test_bootstrap_trees(self):
        calculator = DistanceCalculator("blosum62")
        constructor = DistanceTreeConstructor(calculator)
        trees = list(Consensus.bootstrap_trees(self.alignment, 100, constructor))
        self.assertEqual(len(trees), 100)
        self.assertIsInstance(trees[0], BaseTree.Tree)

    def test_bootstrap_consensus_msa(self):
        calculator = DistanceCalculator("blosum62")
        constructor = DistanceTreeConstructor(calculator, "nj")
        tree = Consensus.bootstrap_consensus(
            self.msa, 100, constructor, Consensus.majority_consensus
        )
        self.assertIsInstance(tree, BaseTree.Tree)
        Phylo.write(tree, os.path.join(temp_dir, "bootstrap_consensus.tre"), "newick")

    def test_bootstrap_consensus(self):
        calculator = DistanceCalculator("blosum62")
        constructor = DistanceTreeConstructor(calculator, "nj")
        tree = Consensus.bootstrap_consensus(
            self.alignment, 100, constructor, Consensus.majority_consensus
        )
        self.assertIsInstance(tree, BaseTree.Tree)
        Phylo.write(tree, os.path.join(temp_dir, "bootstrap_consensus.tre"), "newick")


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)
