#!/usr/bin/env python

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#  Lawrence Berkeley National Laboratory (subject to receipt of any required
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import unittest
from io import StringIO

from weblogo.seq import protein_alphabet
from weblogo.seq_io import clustal_io, phylip_io, plain_io

from . import data_stream


class test_phylip_io(unittest.TestCase):
    def test_read(self) -> None:
        f = data_stream("phylip_test_1.phy")
        seqs = phylip_io.read(f)
        # print seqs
        self.assertEqual(len(seqs), 10)
        self.assertEqual(seqs[0].name, "Cow")
        self.assertEqual(len(seqs[1]), 234)
        f.close()

    def test_iterseq(self) -> None:
        f = data_stream("phylip_test_1.phy")
        n = 0
        for seq in phylip_io.iterseq(f):
            n += 1
        assert n == 10
        f.close()

    def test_parse_plain_fail(self) -> None:
        # should fail with parse error
        f = StringIO(plain_io.example)
        self.assertRaises(ValueError, phylip_io.read, f)

    def test_parse_phylip_test_2(self) -> None:
        f = data_stream("phylip_test_2.phy")
        seqs = phylip_io.read(f)
        self.assertEqual(len(seqs), 6)
        self.assertEqual(len(seqs[0]), 20)
        self.assertEqual(str(seqs[1]), "CGTTACTCGTTGTCGTTACT")
        self.assertEqual(seqs[1].name, "Hesperorni")
        f.close()

    def test_parse_clustal_fail(self) -> None:
        # should fail with parse error
        f = StringIO(clustal_io.example)
        self.assertRaises(ValueError, phylip_io.read, f, protein_alphabet)

    def test_parse_phylip_test_3(self) -> None:
        f = data_stream("phylip_test_3.phy")
        seqs = phylip_io.read(f)
        self.assertEqual(len(seqs), 6)
        self.assertEqual(len(seqs[0]), 20)
        self.assertEqual(str(seqs[1]), "CGTTACTCGTTGTCGTTACT")
        self.assertEqual(seqs[1].name, "Hesperorni")
        f.close()

    def test_parse_phylip_test_4(self) -> None:
        f = data_stream("phylip_test_4.phy")
        seqs = phylip_io.read(f)
        self.assertEqual(len(seqs), 6)
        self.assertEqual(len(seqs[0]), 25)
        self.assertEqual(str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGG")
        self.assertEqual(seqs[2].name, "ddrasa")
        f.close()

    def test_parse_phylip_test_5(self) -> None:
        f = data_stream("phylip_test_5.phy")
        seqs = phylip_io.read(f)
        self.assertEqual(len(seqs), 6)
        self.assertEqual(len(seqs[0]), 50)
        self.assertEqual(
            str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGGGTGGTGGTGGGCGCCGGCCGTGTGG"
        )
        self.assertEqual(seqs[2].name, "ddrasa")
        f.close()

    def test_parse_wrong_phylip_codes_1(self) -> None:
        f = data_stream("phylip_test_6.corrupt.phy")
        self.assertRaises(ValueError, phylip_io.read, f, protein_alphabet)
        f.close()

    def test_parse_wrong_phylip_codes_2(self) -> None:
        f = data_stream("phylip_test_7.corrupt.phy")
        self.assertRaises(ValueError, phylip_io.read, f, protein_alphabet)
        f.close()

    def test_parse_phylip_dna(self) -> None:
        f = data_stream("dna.phy")
        seqs = phylip_io.read(f)
        self.assertEqual(len(seqs), 10)
        self.assertEqual(len(seqs[0]), 705)
        self.assertEqual(str(seqs[1][0:10]), "ATGGCACACC")
        self.assertEqual(seqs[2].name, "Chicken")
        f.close()


if __name__ == "__main__":
    unittest.main()