# Path: alfpy/bbc.py
# def base_base_correlation(seq, k, alphabet=None):
# def create_vectors(seq_records, k=10, alphabet="ATGC"):
#     def __init__(self, vector, disttype='euclid_norm'):
# def main():
#     L = len(alphabet)
#         D = l_dist_correlations - np.dot(p.T, p)
# class Distance(distance.Distance):
# 
# Path: alfpy/utils/distmatrix.py
# def create(id_list, distance):
# def read_highcharts_matrix(id_list, data):
#     def __init__(self, id_list, data):
#     def normalize(self):
#     def __iter__(self):
#     def writer(self, handle, f, decimal_places):
#     def display(self, f="phylip", decimal_places=7):
#     def write_to_file(self, handle, f="phylip", decimal_places=7):
#     def highcharts(self):
#     def format(self, decimal_places=7):
#     def min(self):
#     def max(self):
#     def is_zero(self):
#     def __repr__(self):
# class Matrix():


import unittest
from alfpy import bbc
from alfpy.utils import distmatrix
from . import utils




class VectorTest(unittest.TestCase, utils.ModulesCommonTest):
    """Shared methods and tests for creating BBC vectors."""

    def __init__(self, *args, **kwargs):
        super(VectorTest, self).__init__(*args, **kwargs)
        utils.ModulesCommonTest.set_test_data()

    def test_base_base_correlation_on_dna_k1(self):
        seq = 'CTAGGGAACATACCA'

# Path: alfpy/bbc.py
# def base_base_correlation(seq, k, alphabet=None):
# def create_vectors(seq_records, k=10, alphabet="ATGC"):
#     def __init__(self, vector, disttype='euclid_norm'):
# def main():
#     L = len(alphabet)
#         D = l_dist_correlations - np.dot(p.T, p)
# class Distance(distance.Distance):
# 
# Path: alfpy/utils/distmatrix.py
# def create(id_list, distance):
# def read_highcharts_matrix(id_list, data):
#     def __init__(self, id_list, data):
#     def normalize(self):
#     def __iter__(self):
#     def writer(self, handle, f, decimal_places):
#     def display(self, f="phylip", decimal_places=7):
#     def write_to_file(self, handle, f="phylip", decimal_places=7):
#     def highcharts(self):
#     def format(self, decimal_places=7):
#     def min(self):
#     def max(self):
#     def is_zero(self):
#     def __repr__(self):
# class Matrix():


# Path: tests/test_bbc.py
import unittest
from alfpy import bbc
from alfpy.utils import distmatrix
from . import utils





class VectorTest(unittest.TestCase, utils.ModulesCommonTest):
    """Shared methods and tests for creating BBC vectors."""

    def __init__(self, *args, **kwargs):
        super(VectorTest, self).__init__(*args, **kwargs)
        utils.ModulesCommonTest.set_test_data()

    def test_base_base_correlation_on_dna_k1(self):
        seq = 'CTAGGGAACATACCA'

        vec = bbc.base_base_correlation(seq, 1, utils.ALPHABET_DNA)