# Copyright 2008-2014 by Peter Cock.  All rights reserved.
#
# 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.
"""Tests for Bio.AlignIO.EmbossIO module."""

import unittest
from io import StringIO

from Bio.AlignIO.EmbossIO import EmbossIterator

# http://emboss.sourceforge.net/docs/themes/alnformats/align.simple
with open("Emboss/alignret.txt") as handle:
    simple_example = handle.read()

# http://emboss.sourceforge.net/docs/themes/alnformats/align.pair
with open("Emboss/water.txt") as handle:
    pair_example = handle.read()

with open("Emboss/needle.txt") as handle:
    pair_example2 = handle.read()

with open("Emboss/needle_overhang.txt") as handle:
    pair_example3 = handle.read()


class TestEmbossIO(unittest.TestCase):
    def test_pair_example(self):
        alignments = list(EmbossIterator(StringIO(pair_example)))
        self.assertEqual(len(alignments), 1)
        self.assertEqual(len(alignments[0]), 2)
        self.assertEqual([r.id for r in alignments[0]], ["IXI_234", "IXI_235"])

    def test_simple_example(self):
        alignments = list(EmbossIterator(StringIO(simple_example)))
        self.assertEqual(len(alignments), 1)
        self.assertEqual(len(alignments[0]), 4)
        self.assertEqual(
            [r.id for r in alignments[0]], ["IXI_234", "IXI_235", "IXI_236", "IXI_237"]
        )

    def test_pair_plus_simple(self):
        alignments = list(EmbossIterator(StringIO(pair_example + simple_example)))
        self.assertEqual(len(alignments), 2)
        self.assertEqual(len(alignments[0]), 2)
        self.assertEqual(len(alignments[1]), 4)
        self.assertEqual([r.id for r in alignments[0]], ["IXI_234", "IXI_235"])
        self.assertEqual(
            [r.id for r in alignments[1]], ["IXI_234", "IXI_235", "IXI_236", "IXI_237"]
        )

    def test_pair_example2(self):
        alignments = list(EmbossIterator(StringIO(pair_example2)))
        self.assertEqual(len(alignments), 5)
        self.assertEqual(len(alignments[0]), 2)
        self.assertEqual(
            [r.id for r in alignments[0]], ["ref_rec", "gi|94968718|receiver"]
        )
        self.assertEqual(
            [r.id for r in alignments[4]], ["ref_rec", "gi|94970041|receiver"]
        )

    def test_pair_example3(self):
        alignments = list(EmbossIterator(StringIO(pair_example3)))
        self.assertEqual(len(alignments), 1)
        self.assertEqual(len(alignments[0]), 2)
        self.assertEqual([r.id for r in alignments[0]], ["asis", "asis"])


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