#!/usr/bin/env python
"""Tests of the Enumeration and Alphabet objects.

Note: individual Alphabets are typically in MolType and are tested there.
"""
from cogent.core.alphabet import Enumeration, get_array_type, \
    uint8, uint16, uint32, array, JointEnumeration, CharAlphabet, \
    _make_translation_tables, _make_complement_array
from cogent.core.moltype import RNA

from cogent.util.unit_test import TestCase, main

DnaBases = CharAlphabet('TCAG')
RnaBases = CharAlphabet('UCAG')
AminoAcids = CharAlphabet('ACDEFGHIKLMNPQRSTVWY')

__author__ = "Rob Knight, Peter Maxwell and Gavin Huttley"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Peter Maxwell", "Rob Knight", "Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.3"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"

class translation_table_tests(TestCase):
    """Tests of top-level translation table functions"""
    def test_make_translation_tables(self):
        """_make_translation_tables should translate from chars to indices"""
        a = 'ucag'
        itoa, atoi = _make_translation_tables(a)
        s = 'ggacu'
        obs = s.translate(atoi)
        self.assertEqual(obs, '\x03\x03\x02\x01\x00')
        orig = obs.translate(itoa)
        self.assertEqual(orig, s)

    def test_make_complement_array(self):
        """_make_complement_array should identify complements correctly"""
        complement_array = _make_complement_array(RNA.Alphabet, RNA.Complements)
        test = 'UCAG'
        test_array = [RNA.Alphabet.index(i) for i in test]
        complements = complement_array.take(test_array)
        result = ''.join([RNA.Alphabet[i] for i in complements])
        self.assertEqual(result, 'AGUC')

class get_array_type_tests(TestCase):
    """Tests of the get_array_type top-level function."""
    
    def test_get_array_type(self):
        """get_array_type should return unsigned type that fits elements."""
        self.assertEqual(get_array_type(0), uint8)
        self.assertEqual(get_array_type(100), uint8)
        self.assertEqual(get_array_type(256), uint8)    #boundary case
        self.assertEqual(get_array_type(257), uint16)   #boundary case
        self.assertEqual(get_array_type(10000), uint16)
        self.assertEqual(get_array_type(65536), uint16)
        self.assertEqual(get_array_type(65537), uint32)

class EnumerationTests(TestCase):
    """Tests of the Enumeration object."""
    def test_init(self):
        """Enumeration init should work from any sequence"""
        a = Enumeration('abc')
        self.assertEqual(a.index('a'), 0)
        self.assertEqual(a.index('b'), 1)
        self.assertEqual(a.index('c'), 2)
        self.assertEqual(a[0], 'a')
        self.assertEqual(a[1], 'b')
        self.assertEqual(a[2], 'c')
        self.assertEqual(a.ArrayType, uint8)

        a = Enumeration('bca')
        self.assertEqual(a.index('b'), 0)
        self.assertEqual(a.index('c'), 1)
        self.assertEqual(a.index('a'), 2)
        self.assertEqual(a[0], 'b')
        self.assertEqual(a[1], 'c')
        self.assertEqual(a[2], 'a')

        a = Enumeration([1,'2'])
        self.assertEqual(a.index(1), 0)
        self.assertEqual(a.index('2'), 1)
        self.assertRaises(KeyError, a.index, '1')

        #check that it works with gaps
        a = Enumeration('ab-', '-')
        self.assertEqual(a.Gap, '-')
        self.assertEqual(a.GapIndex, 2)

        a = Enumeration(range(257))    #too big to fit in uint8
        self.assertEqual(a.ArrayType, uint16)

    def test_index(self):
        """Enumeration index should return first index of item"""
        a = Enumeration('bca')
        self.assertEqual(a.index('b'), 0)
        self.assertEqual(a.index('c'), 1)
        self.assertEqual(a.index('a'), 2)

    def test_getitem(self):
        """Enumeration[i] should return character at i"""
        a = Enumeration('bca')
        self.assertEqual(a[0], 'b')
        self.assertEqual(a[1], 'c')
        self.assertEqual(a[2], 'a')

    def test_toIndices(self):
        """Enumeration toIndices should return indices from elements"""
        a = Enumeration('bca')
        self.assertEqual(a.toIndices(''), [])
        self.assertEqual(a.toIndices('ccabac'), [1,1,2,0,2,1])

    def test_isValid(self):
        """Enumeration isValid should return True for valid sequence"""
        a = Enumeration('bca')
        self.assertEqual(a.isValid(''), True)
        self.assertEqual(a.isValid('bbb'), True)
        self.assertEqual(a.isValid('bbbaac'), True)
        self.assertEqual(a.isValid('bbd'), False)
        self.assertEqual(a.isValid('d'), False)
        self.assertEqual(a.isValid(['a', 'b']), True)
        self.assertEqual(a.isValid(['a', None]), False)

    def test_fromIndices(self):
        """Enumeration fromIndices should return elements from indices"""
        a = Enumeration('bca')
        self.assertEqual(a.fromIndices([]), [])
        self.assertEqual(a.fromIndices([1,1,2,0,2,1]), list('ccabac'))

    def test_pow(self):
        """Enumeration pow should produce JointEnumeration with n copies"""
        a = AminoAcids**3
        self.assertEqual(a[0], (AminoAcids[0],)*3)
        self.assertEqual(a[-1], (AminoAcids[-1],)*3)
        self.assertEqual(len(a), len(AminoAcids)**3)
        self.assertEqual(a.ArrayType, uint16)

        #check that it works with gaps
        a = Enumeration('a-b', '-')
        b = a**3
        self.assertEqual(len(b), 27)
        self.assertEqual(b.Gap, ('-','-','-'))
        self.assertEqual(b.GapIndex, 13)
        self.assertEqual(b.ArrayType, uint8)

        #check that array type is set correctly if needed
        b = a**6    #too big to fit in char
        self.assertEqual(b.ArrayType, uint16)

    def test_mul(self):
        """Enumeration mul should produce correct JointEnumeration"""
        a = DnaBases * RnaBases
        self.assertEqual(len(a), 16)
        self.assertEqual(a[0], ('T','U'))
        self.assertEqual(a[-1], ('G','G'))

        #check that it works with gaps
        a = Enumeration('ab-','-')
        b = Enumeration('xz','z')
        x = a*b
        self.assertEqual(x.Gap, ('-','z'))
        self.assertEqual(x.GapIndex, 5)
        self.assertEqual(len(x), 6)
        self.assertEqual(x, (('a','x'),('a','z'),('b','x'),('b','z'),('-','x'),\
            ('-','z')))
        #check that it doesn't work when only one seq has gaps
        c = Enumeration('c')
        x = a*c
        self.assertEqual(x.Gap, None)

    def test_counts(self):
        """Enumeration counts should count freqs in array"""
        a = DnaBases
        f = array([[0,0,1,0,0,3]])
        self.assertEqual(a.counts(f), array([4,1,0,1]))
        #check that it works with byte array
        f = array([[0,0,1,0,0,3]], 'B')
        self.assertEqual(a.counts(f), array([4,1,0,1]))
        #should ignore out-of-bounds items
        g = [0,4]
        self.assertEqual(a.counts(g), array([1,0,0,0]))
        #make sure it works for long sequences, i.e. no wraparound at 255
        h = [0, 3] * 70000
        self.assertEqual(a.counts(h), array([70000,0,0,70000]))
        h2 = array(h).astype('B')
        self.assertEqual(a.counts(h2), array([70000,0,0,70000]))
        i = array([0,3] * 75000)
        self.assertEqual(a.counts(i), array([75000,0,0,75000]))
        #make sure it works for long _binary_ sequences, e.g. the results
        #of array comparisons.
        a = array([0,1,2,3]*10000)
        b = array([0,0,0,0]*10000)
        same = (a==b)

class CharAlphabetTests(TestCase):
    """Tests of CharAlphabets."""
    def test_init(self):
        """CharAlphabet init should make correct translation tables"""
        r = CharAlphabet('UCAG')
        i2c, c2i = r._indices_to_chars, r._chars_to_indices
        s = array([0,0,1,0,3,2], 'b').tostring()
        self.assertEqual(s.translate(i2c), 'UUCUGA')
        self.assertEqual('UUCUGA'.translate(c2i), '\000\000\001\000\003\002')
        
    def test_fromString(self):
        """CharAlphabet fromString should return correct array"""
        r = CharAlphabet('UCAG')
        self.assertEqual(r.fromString('UUCUGA'), array([0,0,1,0,3,2],'B'))

    def test_isValid(self):
        """CharAlphabet isValid should return True for valid sequence"""
        a = CharAlphabet('bca')
        self.assertEqual(a.isValid(''), True)
        self.assertEqual(a.isValid('bbb'), True)
        self.assertEqual(a.isValid('bbbaac'), True)
        self.assertEqual(a.isValid('bbd'), False)
        self.assertEqual(a.isValid('d'), False)
        self.assertEqual(a.isValid(['a', 'b']), True)
        self.assertEqual(a.isValid(['a', None]), False)


    def test_fromArray(self):
        """CharAlphabet fromArray should return correct array"""
        r = CharAlphabet('UCAG')
        self.assertEqual(r.fromArray(array(['UUC','UGA'], 'c')), \
            array([[0,0,1],[0,3,2]], 'B'))

    def test_toChars(self):
        """CharAlphabet toChars should convert an input array to chars"""
        r = CharAlphabet('UCAG')
        c = r.toChars(array([[0,0,1],[0,3,2]], 'B'))
        self.assertEqual(c, \
            array(['UUC','UGA'], 'c'))

    def test_toString(self):
        """CharAlphabet toString should convert an input array to string"""
        r = CharAlphabet('UCAG')
        self.assertEqual(r.toString(array([[0,0,1],[0,3,2]], 'B')), 'UUC\nUGA')
        #should work with single seq
        self.assertEqual(r.toString(array([[0,0,1,0,3,2]], 'B')), 'UUCUGA')
        #should work with single seq
        self.assertEqual(r.toString(array([0,0,1,0,3,2], 'B')), 'UUCUGA')
        #should work with empty seq
        self.assertEqual(r.toString(array([], 'B')), '')
        
    def test_pairs(self):
        """pairs should cache the same object."""
        r = CharAlphabet('UCAG')
        rp = r.Pairs
        self.assertEqual(len(rp), 16)
        rp2 = r.Pairs
        self.assertSameObj(rp, rp2)

    def test_triples(self):
        """triples should cache the same object."""
        r = CharAlphabet('UCAG')
        rt = r.Triples
        self.assertEqual(len(rt), 64)
        rt2 = r.Triples
        self.assertSameObj(rt, rt2)


class JointEnumerationTests(TestCase):
    """Tests of JointEnumerations."""
    def test_init(self):
        """JointEnumeration init should work as expected"""
        #should work for alphabet object
        a = JointEnumeration([DnaBases, RnaBases])
        self.assertEqual(len(a), 16)
        self.assertEqual(a.Shape, (4,4))
        self.assertEqual(a[0], ('T','U'))
        self.assertEqual(a[-1], ('G','G'))
        self.assertEqual(a._sub_enum_factors, array([[4],[1]]))

        #should work for arbitrary sequences
        a = JointEnumeration(['TCAG', 'UCAG'])
        self.assertEqual(len(a), 16)
        self.assertEqual(a[0], ('T','U'))
        self.assertEqual(a[-1], ('G','G'))
        self.assertEqual(a._sub_enum_factors, array([[4],[1]]))

        #should work for different length sequences
        a = JointEnumeration(['TCA', 'UCAG'])
        self.assertEqual(a.Shape, (3,4))
        self.assertEqual(len(a), 12)
        self.assertEqual(a[0], ('T','U'))
        self.assertEqual(a[-1], ('A','G'))
        self.assertEqual(a._sub_enum_factors, \
            array([[4],[1]])) #note: _not_ [3,1]

    def test_toIndices(self):
        """JointEnumeration toIndices should convert tuples correctly"""
        a = JointEnumeration(['TCAG','UCAG'])
        i = a.toIndices([('T','U'),('G','G'),('G','G')])
        self.assertEqual(i, [0, 15, 15])

    def test_fromIndices(self):
        """JointEnumeration fromIndices should return correct tuples"""
        a = JointEnumeration(['TCAG','UCAG'])
        i = a.fromIndices([0, 15, 15])
        self.assertEqual(i, [('T','U'),('G','G'),('G','G')])

    def test_packArrays(self):
        """JointEnumeration packArrays should return correct array."""
        a = JointEnumeration(['xyz', 'abcd', 'ef'])
        v = [[0,1,2,0],[3,3,1,0], [1,1,0,0]]
        result = a.packArrays(v)
        self.assertEqual(result, array([7,15,18,0]))
        
    def test_unpackArrays(self):
        """JointEnumeration unpackArrays should return correct arrays."""
        a = JointEnumeration(['xyz', 'abcd', 'ef'])
        v = [7,15,18,0]
        result = a.unpackArrays(v)
        self.assertEqual(result, array([[0,1,2,0],[3,3,1,0], [1,1,0,0]]))

if __name__ == '__main__':
    main()
