#!/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 dna_alphabet, protein_alphabet
from weblogo.seq_io import clustal_io, nbrf_io, plain_io

from . import data_stream


class test_nbrf_io(unittest.TestCase):
    def test_parse_cox2(self) -> None:
        f = data_stream("cox2.nbrf")
        seqs = nbrf_io.read(f)
        self.assertEqual(len(seqs), 5)
        self.assertEqual(len(seqs[1]), 210)
        self.assertEqual(
            str(seqs[0]),
            "MAFILSFWMIFLLDSVIVLLSFVCFVCVWICALLFSTVLLVSKLNNIYCTWDFTASKFIDVYWFTIGGMFSLG"
            "LLLRLCLLLYFGHLNFVSFDLCKVVGFQWYWVYFIFGETTIFSNLILESDYMIGDLRLLQCNHVLTLLSLVIY"
            "KLWLSAVDVIHSFAISSLGVKVENLVAVMK",
        )
        self.assertEqual(seqs[0].alphabet, protein_alphabet)
        f.close()

    def test_parse_crab(self) -> None:
        f = data_stream("crab.nbrf")
        seqs = nbrf_io.read(f)
        self.assertEqual(seqs[0].alphabet, protein_alphabet)
        self.assertEqual(len(seqs), 9)
        self.assertEqual(seqs[2].name, "CRAB_CHICK")
        self.assertEqual(
            seqs[2].description, "ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN)."
        )
        f.close()

    def test_parse_dna(self) -> None:
        f = data_stream("dna.pir")
        seqs = nbrf_io.read(f)
        self.assertEqual(seqs[0].alphabet, dna_alphabet)
        self.assertEqual(len(seqs), 10)
        f.close()

    def test_parse_examples(self) -> None:
        f = data_stream("rhod.pir")
        seqs = nbrf_io.read(f)
        self.assertEqual(seqs[0].alphabet, protein_alphabet)
        self.assertEqual(len(seqs), 3)
        f.close()

    def test_parse_protein(self) -> None:
        f = data_stream("protein.pir")
        seqs = nbrf_io.read(f)
        self.assertEqual(seqs[0].alphabet, protein_alphabet)
        self.assertEqual(len(seqs), 10)
        f.close()

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

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

    def test_pir_file_from_clustal(self) -> None:
        f = data_stream("clustalw.pir")
        seqs = nbrf_io.read(f)
        self.assertEqual(len(seqs), 2)
        self.assertEqual(
            seqs[1].endswith(
                "C-AATC-G-CAATG-G--CTTGAACCGGGTAAAAGTCGT-A----------------------------------------"
                "-----------------------------------------"
            ),
            True,
        )
        f.close()

    def test_parse_examples_alphabet(self) -> None:
        f = data_stream("rhod.pir")
        seqs = nbrf_io.read(f, alphabet=protein_alphabet)
        self.assertEqual(seqs[0].alphabet, protein_alphabet)
        self.assertEqual(len(seqs), 3)
        f.close()


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