#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Unit test for pm."""

import sys
import unittest
from os.path import dirname, realpath

from pm import analyze
from pm.status import Y, Conserved, PM, NA
from pm.pattern import TranslatedPattern, PlainPattern


class RoutineTest(unittest.TestCase):
    """RoutineTest"""

    def test_analyze_with_Y(self):
        """pm.analyze should give the expection value"""

        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'

        status = analyze(seq, stdseq)
        self.assertEqual(status, Y(stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_Conserved(self):
        """pm.analyze should give the expection value"""

        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCC'

        status = analyze(seq, stdseq)
        self.assertEqual(status, Conserved(nt_pm=1, stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_PM(self):
        """pm.analyze should give the expection value"""

        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAAACT'

        status = analyze(seq, stdseq)
        self.assertEqual(status, PM(nt_pm=1, aa_pm=1, stdseq=stdseq))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, 1)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_NA(self):
        """pm.analyze should give the expection value"""

        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGC-TT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'

        status = analyze(seq, stdseq)
        self.assertEqual(status, NA(gaps=1, stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 1)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_Y_with_nontranslate(self):
        """pm.analyze should give the expection value"""

        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'

        status = analyze(seq, stdseq, translate=False)
        self.assertEqual(status, Y(stdseq=stdseq, nt_pm=0, gaps=0, aa_pm=None))
        self.assertEqual(status.seq, seq.replace('-', ''))
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, None)
        self.assertIsInstance(status.pattern, PlainPattern)

    def test_analyze_with_NA_with_nontranslate(self):
        """pm.analyze should give the expection value"""

        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCC'

        status = analyze(seq, stdseq, translate=False)
        self.assertEqual(status, NA(nt_pm=1, aa_pm=None, gaps=0, stdseq=stdseq))
        self.assertEqual(status.seq, seq.replace('-', ''))
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, None)
        self.assertIsInstance(status.pattern, PlainPattern)


if __name__ == '__main__':
    unittest.main()
0cf670e309c30e5caddae655e946765bd227370c
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class RoutineTest(unittest.TestCase):
    <mask token>
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    def test_analyze_with_Conserved(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCC'
        status = analyze(seq, stdseq)
        self.assertEqual(status, Conserved(nt_pm=1, stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)
    <mask token>
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    def test_analyze_with_Y_with_nontranslate(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        status = analyze(seq, stdseq, translate=False)
        self.assertEqual(status, Y(stdseq=stdseq, nt_pm=0, gaps=0, aa_pm=None))
        self.assertEqual(status.seq, seq.replace('-', ''))
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, None)
        self.assertIsInstance(status.pattern, PlainPattern)

    def test_analyze_with_NA_with_nontranslate(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCC'
        status = analyze(seq, stdseq, translate=False)
        self.assertEqual(status, NA(nt_pm=1, aa_pm=None, gaps=0, stdseq=stdseq)
            )
        self.assertEqual(status.seq, seq.replace('-', ''))
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, None)
        self.assertIsInstance(status.pattern, PlainPattern)


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<mask token>


class RoutineTest(unittest.TestCase):
    <mask token>

    def test_analyze_with_Y(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        status = analyze(seq, stdseq)
        self.assertEqual(status, Y(stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_Conserved(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCC'
        status = analyze(seq, stdseq)
        self.assertEqual(status, Conserved(nt_pm=1, stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)
    <mask token>

    def test_analyze_with_NA(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGC-TT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        status = analyze(seq, stdseq)
        self.assertEqual(status, NA(gaps=1, stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 1)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_Y_with_nontranslate(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        status = analyze(seq, stdseq, translate=False)
        self.assertEqual(status, Y(stdseq=stdseq, nt_pm=0, gaps=0, aa_pm=None))
        self.assertEqual(status.seq, seq.replace('-', ''))
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, None)
        self.assertIsInstance(status.pattern, PlainPattern)

    def test_analyze_with_NA_with_nontranslate(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCC'
        status = analyze(seq, stdseq, translate=False)
        self.assertEqual(status, NA(nt_pm=1, aa_pm=None, gaps=0, stdseq=stdseq)
            )
        self.assertEqual(status.seq, seq.replace('-', ''))
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, None)
        self.assertIsInstance(status.pattern, PlainPattern)


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class RoutineTest(unittest.TestCase):
    """RoutineTest"""

    def test_analyze_with_Y(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        status = analyze(seq, stdseq)
        self.assertEqual(status, Y(stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_Conserved(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCC'
        status = analyze(seq, stdseq)
        self.assertEqual(status, Conserved(nt_pm=1, stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_PM(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAAACT'
        status = analyze(seq, stdseq)
        self.assertEqual(status, PM(nt_pm=1, aa_pm=1, stdseq=stdseq))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, 1)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_NA(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGC-TT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        status = analyze(seq, stdseq)
        self.assertEqual(status, NA(gaps=1, stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 1)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_Y_with_nontranslate(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        status = analyze(seq, stdseq, translate=False)
        self.assertEqual(status, Y(stdseq=stdseq, nt_pm=0, gaps=0, aa_pm=None))
        self.assertEqual(status.seq, seq.replace('-', ''))
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, None)
        self.assertIsInstance(status.pattern, PlainPattern)

    def test_analyze_with_NA_with_nontranslate(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCC'
        status = analyze(seq, stdseq, translate=False)
        self.assertEqual(status, NA(nt_pm=1, aa_pm=None, gaps=0, stdseq=stdseq)
            )
        self.assertEqual(status.seq, seq.replace('-', ''))
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, None)
        self.assertIsInstance(status.pattern, PlainPattern)


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class RoutineTest(unittest.TestCase):
    """RoutineTest"""

    def test_analyze_with_Y(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        status = analyze(seq, stdseq)
        self.assertEqual(status, Y(stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_Conserved(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCC'
        status = analyze(seq, stdseq)
        self.assertEqual(status, Conserved(nt_pm=1, stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_PM(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAAACT'
        status = analyze(seq, stdseq)
        self.assertEqual(status, PM(nt_pm=1, aa_pm=1, stdseq=stdseq))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, 1)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_NA(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGC-TT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        status = analyze(seq, stdseq)
        self.assertEqual(status, NA(gaps=1, stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 1)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_Y_with_nontranslate(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        status = analyze(seq, stdseq, translate=False)
        self.assertEqual(status, Y(stdseq=stdseq, nt_pm=0, gaps=0, aa_pm=None))
        self.assertEqual(status.seq, seq.replace('-', ''))
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, None)
        self.assertIsInstance(status.pattern, PlainPattern)

    def test_analyze_with_NA_with_nontranslate(self):
        """pm.analyze should give the expection value"""
        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCC'
        status = analyze(seq, stdseq, translate=False)
        self.assertEqual(status, NA(nt_pm=1, aa_pm=None, gaps=0, stdseq=stdseq)
            )
        self.assertEqual(status.seq, seq.replace('-', ''))
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, None)
        self.assertIsInstance(status.pattern, PlainPattern)


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

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Unit test for pm."""

import sys
import unittest
from os.path import dirname, realpath

from pm import analyze
from pm.status import Y, Conserved, PM, NA
from pm.pattern import TranslatedPattern, PlainPattern


class RoutineTest(unittest.TestCase):
    """RoutineTest"""

    def test_analyze_with_Y(self):
        """pm.analyze should give the expection value"""

        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'

        status = analyze(seq, stdseq)
        self.assertEqual(status, Y(stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_Conserved(self):
        """pm.analyze should give the expection value"""

        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCC'

        status = analyze(seq, stdseq)
        self.assertEqual(status, Conserved(nt_pm=1, stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_PM(self):
        """pm.analyze should give the expection value"""

        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAAACT'

        status = analyze(seq, stdseq)
        self.assertEqual(status, PM(nt_pm=1, aa_pm=1, stdseq=stdseq))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, 1)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_NA(self):
        """pm.analyze should give the expection value"""

        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGC-TT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'

        status = analyze(seq, stdseq)
        self.assertEqual(status, NA(gaps=1, stdseq=stdseq, aa_pm=0))
        self.assertEqual(status.seq, seq)
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 1)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, 0)
        self.assertIsInstance(status.pattern, TranslatedPattern)

    def test_analyze_with_Y_with_nontranslate(self):
        """pm.analyze should give the expection value"""

        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGTT'

        status = analyze(seq, stdseq, translate=False)
        self.assertEqual(status, Y(stdseq=stdseq, nt_pm=0, gaps=0, aa_pm=None))
        self.assertEqual(status.seq, seq.replace('-', ''))
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 0)
        self.assertEqual(status.aa_pm, None)
        self.assertIsInstance(status.pattern, PlainPattern)

    def test_analyze_with_NA_with_nontranslate(self):
        """pm.analyze should give the expection value"""

        seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCT'
        stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCTGGCGCC'

        status = analyze(seq, stdseq, translate=False)
        self.assertEqual(status, NA(nt_pm=1, aa_pm=None, gaps=0, stdseq=stdseq))
        self.assertEqual(status.seq, seq.replace('-', ''))
        self.assertEqual(status.stdseq, stdseq)
        self.assertEqual(status.gaps, 0)
        self.assertEqual(status.length, len(seq))
        self.assertEqual(status.nt_pm, 1)
        self.assertEqual(status.aa_pm, None)
        self.assertIsInstance(status.pattern, PlainPattern)


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