# Copyright 2002 by Katharine Lindner.  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.

# python unittest framework
"""Tests for Crystal module (OBSOLETE)."""

import unittest
import copy
import warnings

from Bio import BiopythonDeprecationWarning

with warnings.catch_warnings():
    warnings.simplefilter("ignore", BiopythonDeprecationWarning)
    # modules to be tested
    from Bio.Crystal import Hetero, Chain, Crystal, CrystalError


class ChainTestCase(unittest.TestCase):
    def setUp(self):
        self.a = "C A A C T A G G T C A C U A G G T C A G"
        self.b = "C T G A C C T A G T G A C C T A G T T G"
        self.c = "THR LYS LEU ASN GLY MET VAL LEU LEU CYS LYS VAL CYS GLY ASP"
        self.d = "THR LYS LEU ASN GLY MET VAL LEU LEU CYS LYS VAL CYS GLY ASP "
        self.e = "TYR LYS LEU ASN GLY MET VAL LEU LEU CYS LYS VAL CYS GLY ASP "
        self.f = "THR LYS LEU ASN GLY MET VAL LEU LEU CYS LYS VAL CYS GLY SER "
        self.g = "C A A C T A G G T C A C U A G G T C A T"
        self.h = "G A A C T A G G T C A C U A G G T C A G"

    def testEquals(self):
        first = Chain(self.a)
        second = Chain(self.a)
        self.assertEqual(first, second)

        first = Chain(self.b)
        second = Chain(self.b)
        self.assertEqual(first, second)

        first = Chain(self.c)
        second = Chain(self.c)
        self.assertEqual(first, second)

        first = Chain(self.a)
        second = Chain(self.g)
        self.assertNotEqual(first, second)

        first = Chain(self.a)
        second = Chain(self.h)
        self.assertNotEqual(first, second)

        first = Chain(self.c)
        second = Chain(self.e)
        self.assertNotEqual(first, second)

        first = Chain(self.c)
        second = Chain(self.f)
        self.assertNotEqual(first, second)

    def testLen(self):
        chain = Chain(self.a)
        elements = self.a.strip().split()
        num_elements = len(elements)
        self.assertEqual(len(chain), num_elements)

        chain = Chain(self.b)
        elements = self.b.strip().split()
        num_elements = len(elements)
        self.assertEqual(len(chain), num_elements)

        chain = Chain(self.c)
        elements = self.c.strip().split()
        num_elements = len(elements)
        self.assertEqual(len(chain), num_elements)

    def testAppend(self):
        chain = Chain(self.a[:])
        chain.append("U")
        elements = self.a.strip().split()
        num_elements = len(elements)
        last_element = chain.data[-1]
        self.assertEqual("u", last_element.data)
        self.assertEqual(len(chain), num_elements + 1)

        chain = Chain(self.a[:])
        chain.append(Hetero("A"))
        elements = self.a.strip().split()
        num_elements = len(elements)
        last_element = chain.data[-1]
        self.assertEqual("a", last_element.data)
        self.assertEqual(len(chain), num_elements + 1)

        chain = Chain(self.b[:])
        chain.append("t")
        elements = self.b.strip().split()
        num_elements = len(elements)
        last_element = chain.data[-1]
        self.assertEqual("t", last_element.data)
        self.assertEqual(len(chain), num_elements + 1)

        chain = Chain(self.b[:])
        chain.append(Hetero("C"))
        elements = self.b.strip().split()
        num_elements = len(elements)
        last_element = chain.data[-1]
        self.assertEqual("c", last_element.data)
        self.assertEqual(len(chain), num_elements + 1)

        chain = Chain(self.c[:])
        chain.append("ser")
        elements = self.c.strip().split()
        num_elements = len(elements)
        last_element = chain.data[-1]
        self.assertEqual("ser", last_element.data)
        self.assertEqual(len(chain), num_elements + 1)

    def testInsert(self):
        chain = Chain(self.a[:])
        i = 4
        chain.insert(i, "g")
        elements = self.a.strip().split()
        num_elements = len(elements)
        target_element = chain.data[i]
        self.assertEqual("g", target_element.data)
        self.assertEqual(len(chain), num_elements + 1)

        chain = Chain(self.a[:])
        i = 0
        chain.insert(i, "t")
        elements = self.a.strip().split()
        num_elements = len(elements)
        target_element = chain.data[i]
        self.assertEqual("t", target_element.data)
        self.assertEqual(len(chain), num_elements + 1)

        chain = Chain(self.b[:])
        i = 9
        chain.insert(i, Hetero("a"))
        elements = self.a.strip().split()
        num_elements = len(elements)
        target_element = chain.data[i]
        self.assertEqual("a", target_element.data)
        self.assertEqual(len(chain), num_elements + 1)

        chain = Chain(self.c[:])
        i = 5
        chain.insert(i, "gln")
        elements = self.c.strip().split()
        num_elements = len(elements)
        target_element = chain.data[i]
        self.assertEqual("gln", target_element.data)
        self.assertEqual(len(chain), num_elements + 1)

    def testRemove(self):

        chain = Chain(self.a[:])
        elements = self.a.strip().split()
        num_elements = len(elements)
        num_a = chain.data.count(Hetero("a"))
        chain.remove("a")
        num_a_remaining = chain.data.count(Hetero("a"))
        self.assertEqual(num_a_remaining, num_a - 1)
        self.assertEqual(len(chain), num_elements - 1)

        chain = Chain(self.b[:])
        elements = self.b.strip().split()
        num_elements = len(elements)
        num_b = chain.data.count(Hetero("t"))
        chain.remove("t")
        num_b_remaining = chain.data.count(Hetero("t"))
        self.assertEqual(num_b_remaining, num_b - 1)
        self.assertEqual(len(chain), num_elements - 1)

        chain = Chain(self.c[:])
        elements = self.c.strip().split()
        num_elements = len(elements)
        num_leu = chain.data.count(Hetero("leu"))
        chain.remove("leu")
        num_leu_remaining = chain.data.count(Hetero("leu"))
        self.assertEqual(num_leu_remaining, num_leu - 1)
        self.assertEqual(len(chain), num_elements - 1)

    def testCount(self):
        chain = Chain(self.a[:])
        num_a = chain.data.count(Hetero("a"))
        self.assertEqual(chain.count("a"), num_a)

        chain = Chain(self.b[:])
        num_a = chain.data.count(Hetero("t"))
        self.assertEqual(chain.count("t"), num_a)

        chain = Chain(self.c[:])
        num_a = chain.data.count(Hetero("leu"))
        self.assertEqual(chain.count("leu"), num_a)

        chain = Chain(self.c[:])
        num_a = chain.data.count(Hetero("cys"))
        self.assertEqual(chain.count("cys"), num_a)

    def testIndex(self):
        chain = Chain(self.a[:])
        index_g = chain.data.index(Hetero("g"))
        self.assertEqual(chain.index("g"), index_g)

        chain = Chain(self.b[:])
        index_c = chain.data.index(Hetero("c"))
        self.assertEqual(chain.index("c"), index_c)

        chain = Chain(self.c[:])
        index_met = chain.data.index(Hetero("met"))
        self.assertEqual(chain.index("met"), index_met)

    def testGetItem(self):
        chain = Chain(self.a[:])
        element_3 = chain.data[3]
        self.assertEqual(chain[3], element_3)

        chain = Chain(self.a[:])
        element_0 = chain.data[0]
        self.assertEqual(chain[0], element_0)

        chain = Chain(self.b[:])
        element_7 = chain.data[7]
        self.assertEqual(chain[7], element_7)

        chain = Chain(self.b[:])
        last_element = chain.data[-1]
        self.assertEqual(chain[-1], last_element)

        chain = Chain(self.c[:])
        element_8 = chain.data[8]
        self.assertEqual(chain[8], element_8)

    def testSetItem(self):
        chain = Chain(self.a[:])
        chain[2] = "t"
        element_2 = chain.data[2]
        self.assertEqual(chain[2], element_2)

        chain = Chain(self.a[:])
        chain[0] = Hetero("U")
        element_0 = chain.data[0]
        self.assertEqual(chain[0], element_0)

        chain = Chain(self.b[:])
        chain[-1] = Hetero("c")
        last_element = chain.data[-1]
        self.assertEqual(chain[-1], last_element)

        chain = Chain(self.b[:])
        chain[1] = "a"
        element_1 = chain.data[1]
        self.assertEqual(chain[1], element_1)

        chain = Chain(self.c[:])
        chain[5] = "ser"
        element_5 = chain.data[5]
        self.assertEqual(chain[5], element_5)

    def testDelItem(self):

        chain = Chain(self.a[:])
        elements = self.a.strip().split()
        num_elements = len(elements)
        num_t = chain.data.count(Hetero("t"))
        del chain[4]
        num_t_remaining = chain.data.count(Hetero("t"))
        self.assertEqual(num_t_remaining, num_t - 1)
        self.assertEqual(len(chain), num_elements - 1)

        chain = Chain(self.a[:])
        elements = self.a.strip().split()
        num_elements = len(elements)
        num_u = chain.data.count(Hetero("u"))
        del chain[12]
        num_u_remaining = 0
        self.assertEqual(num_u_remaining, num_u - 1)
        self.assertEqual(len(chain), num_elements - 1)

        chain = Chain(self.b[:])
        elements = self.b.strip().split()
        num_elements = len(elements)
        num_c = chain.data.count(Hetero("c"))
        del chain[0]
        num_c_remaining = chain.data.count(Hetero("c"))
        self.assertEqual(num_c_remaining, num_c - 1)
        self.assertEqual(len(chain), num_elements - 1)

        chain = Chain(self.b[:])
        elements = self.b.strip().split()
        num_elements = len(elements)
        num_g = chain.data.count(Hetero("t"))
        del chain[6]
        num_g_remaining = chain.data.count(Hetero("t"))
        self.assertEqual(num_g_remaining, num_g - 1)
        self.assertEqual(len(chain), num_elements - 1)

        chain = Chain(self.c[:])
        elements = self.c.strip().split()
        num_elements = len(elements)
        num_thr = chain.data.count(Hetero("thr"))
        del chain[0]
        num_thr_remaining = chain.data.count(Hetero("thr"))
        self.assertEqual(num_thr_remaining, num_thr - 1)
        self.assertEqual(len(chain), num_elements - 1)

    def testGetSlice(self):
        chain = Chain(self.a[:])
        first = 0
        last = len(chain)
        slice = chain[:]
        other = chain.data[:]
        self.assertEqual(slice.data, other)

        chain = Chain(self.a[:])
        first = 0
        last = 4
        slice = chain[first:last]
        other = chain.data[first:last]
        self.assertEqual(slice.data, other)

        chain = Chain(self.b[:])
        first = 2
        last = len(chain)
        slice = chain[first:last]
        other = chain.data[first:last]
        self.assertEqual(slice.data, other)

        chain = Chain(self.b[:])
        first = -1
        slice = chain[first:]
        other = chain.data[first:]
        self.assertEqual(slice.data, other)

        chain = Chain(self.c[:])
        first = 3
        last = 7
        slice = chain[first:last]
        other = chain.data[first:last]
        self.assertEqual(slice.data, other)

        chain = Chain(self.c[:])
        first = 3
        last = -1
        slice = chain[first:last]
        other = chain.data[first:last]
        self.assertEqual(slice.data, other)

    def testSetSlice(self):
        chain = Chain(self.a[:])
        slice = "G T C A G 5NC G C A T G G"
        chain[:] = slice[4:7]
        other = Chain(slice[4:7])
        self.assertEqual(chain, other)

        chain = Chain(self.c[:])
        old_chain = Chain(self.c[:])
        slice = "MET ILE GLU ILE LYS ASP"
        chain[2:5] = slice
        other = Chain(old_chain.data[:2] + Chain(slice).data + old_chain.data[5:])
        self.assertEqual(chain, other)

        chain = Chain(self.c[:])
        old_chain = Chain(self.c[:])
        slice = "CYS GLY ALA GLU CYS VAL TYR"
        chain[7:] = slice
        other = Chain(old_chain.data[:7] + Chain(slice).data)
        self.assertEqual(chain, other)

        chain = Chain(self.c[:])
        old_chain = Chain(self.c[:])
        slice = "SER ASN GLU TRP ASP "
        chain[:9] = slice
        other = Chain(Chain(slice).data + old_chain.data[9:])
        self.assertEqual(chain, other)

    def testDelSlice(self):
        chain = Chain(self.c[:])
        old_chain = Chain(self.c[:])
        del chain[3:8]
        other = Chain(old_chain.data[:3] + old_chain.data[8:])
        self.assertEqual(chain, other)

        chain = Chain(self.c[:])
        old_chain = Chain(self.c[:])
        del chain[:4]
        other = Chain(old_chain.data[4:])
        self.assertEqual(chain, other)

        chain = Chain(self.c[:])
        old_chain = Chain(self.c[:])
        del chain[9:]
        other = Chain(old_chain.data[:9])
        self.assertEqual(chain, other)

    def testContains(self):
        chain = Chain(self.c[:])
        self.assertNotIn("ser", chain)
        self.assertIn("lys", chain)
        self.assertIn("asp", chain)

    def testAdd(self):
        texta = "G U G G U C U G A U G A G G C C"
        textb = "G G C C G A A A C U C G U A A G A G U C A C C A C"
        targeta = texta + Chain(textb)
        targetb = Chain(texta) + textb
        targetc = Chain(texta) + Chain(textb)
        self.assertEqual(targeta, targetc)
        self.assertEqual(targetb, targetc)
        self.assertEqual(targeta, targetb)
        self.assertEqual(len(targeta), len(Chain(texta)) + len(Chain(textb)))

        targetd = Chain(texta)
        targetd += textb

        targete = Chain(texta)
        targete += Chain(textb)
        self.assertEqual(targetd, targetc)
        self.assertEqual(targete, targetb)


class CrystalTestCase(unittest.TestCase):
    def setUp(self):

        self.crystal = Crystal(
            {
                "a": "T T G A C T C T C T T A A",
                "b": Chain("G A G A G T C A"),
                "c": "T T G A C T C T C T T A A",
                "d": Chain("G A G A G T C A"),
            }
        )

    def testLen(self):
        self.assertEqual(len(self.crystal), len(self.crystal.data))

    def testGetItem(self):
        self.assertEqual(self.crystal["a"], self.crystal.data["a"])

    def testSetItem(self):
        target = copy.deepcopy(self.crystal)
        e = "MET ALA LEU THR ASN ALA GLN ILE LEU ALA VAL ILE ASP SER"
        f = "LEU GLY GLY GLY LEU GLN GLY THR LEU HIS CYS TYR GLU ILE PRO LEU"
        target["e"] = e
        target["f"] = Chain(f)
        self.assertEqual(Chain(e), target["e"])
        self.assertEqual(Chain(f), target["f"])

    def testDelItem(self):
        target = copy.deepcopy(self.crystal)
        del target["b"]
        self.assertNotIn("b", target.data)
        self.assertIn("a", target.data)
        self.assertIn("c", target.data)

    def testClear(self):
        target = copy.deepcopy(self.crystal)
        target.clear()
        self.assertEqual(len(target.data), 0)

    def testKeys(self):
        self.assertEqual(list(self.crystal.keys()), list(self.crystal.data.keys()))

    def testValues(self):
        self.assertEqual(list(self.crystal.values()), list(self.crystal.data.values()))

    def testItems(self):
        self.assertEqual(list(self.crystal.items()), list(self.crystal.data.items()))

    def testHasKey(self):
        self.assertIn("b", self.crystal)
        self.assertIn("c", self.crystal)
        self.assertNotIn("z", self.crystal)


class HeteroTestCase(unittest.TestCase):
    def testInit(self):
        self.assertRaises(CrystalError, Hetero, "abcd")
        self.assertRaises(CrystalError, Hetero, "")
        self.assertRaises(CrystalError, Hetero, "A@#")
        self.assertRaises(CrystalError, Hetero, [])
        self.assertRaises(CrystalError, Hetero, {})

    def testLen(self):
        bru = Hetero("bru")
        self.assertEqual(len(bru), 3)
        _14w = Hetero("14w")
        self.assertEqual(len(_14w), 3)
        a = Hetero("a")
        self.assertEqual(len(a), 1)
        ga = Hetero("ga")
        self.assertEqual(len(ga), 2)

    def testEquals(self):
        u = Hetero("u")
        u1 = Hetero("u")
        self.assertEqual(u, u1)
        self.assertEqual(u, Hetero("U"))
        self.assertNotEqual(u, Hetero("u1"))
        self.assertNotEqual(u, Hetero("x"))
        gna = Hetero("gna")
        self.assertEqual(gna, Hetero("gNA"))
        self.assertEqual(gna, Hetero("GnA"))
        self.assertNotEqual(gna, Hetero("gnb"))
        self.assertNotEqual(gna, Hetero("na"))


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