# Copyright 2007 by Tiago Antao.  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.

"""Utility code for using SimCoal (DEPRECATED)."""

from __future__ import print_function

from os import sep
import re
from functools import reduce

from Bio.PopGen.SimCoal import builtin_tpl_dir


def exec_template(template):
    executed_template = template
    match = re.search('!!!(.*?)!!!', executed_template, re.MULTILINE)
    # while len(match.groups())>0:
    while match:
        exec_result = str(eval(match.groups()[0]))
        executed_template = executed_template.replace(
               '!!!' + match.groups()[0] + '!!!',
               exec_result, 1)
        match = re.search('!!!(.*?)!!!', executed_template, re.MULTILINE)
        # match = patt.matcher(String(executed_template))
    return executed_template


def process_para(in_string, out_file_prefix, para_list, curr_values):
    if (para_list == []):
        template = in_string
        f_name = out_file_prefix
        # f_name += '_' + str(total_size)
        for tup in curr_values:
            name, val = tup
            f_name += '_' + str(val)
            # reg = re.compile('\?' + name, re.MULTILINE)
            # template = re.sub(reg, str(val), template)
            template = template.replace('?' + name, str(val))
        with open(f_name + '.par', 'w') as f:
            # executed_template = template
            executed_template = exec_template(template)
            clean_template = executed_template.replace('\r\n', '\n').replace('\n\n', '\n')
            f.write(clean_template)
        return [f_name]
    else:
        name, rng = para_list[0]
        fnames = []
        for val in rng:
            new_values = [(name, val)]
            new_values.extend(curr_values)
            more_names = process_para(in_string, out_file_prefix, para_list[1:], new_values)
            fnames.extend(more_names)
        return fnames


def dupe(motif, times):
    ret_str = ''
    for i in range(1, times + 1):
        ret_str += motif + '\r\n'
    return ret_str


def get_xy_from_matrix(x_max, y_max, pos):
    y = (pos - 1) / x_max
    x = (pos - 1) % x_max
    return x, y


def get_step_2d(x_max, y_max, x, y, mig):
    my_x, my_y = get_xy_from_matrix(x_max, y_max, y)
    other_x, other_y = get_xy_from_matrix(x_max, y_max, x)

    if (my_x - other_x) ** 2 + (my_y - other_y) ** 2 == 1:
        return str(mig) + ' '
    else:
        return '0 '


def generate_ssm2d_mat(x_max, y_max, mig):
    mig_mat = ''
    for x in range(1, x_max * y_max + 1):
        for y in range(1, x_max * y_max + 1):
            mig_mat += get_step_2d(x_max, y_max, x, y, mig)
        mig_mat += "\r\n"
    return mig_mat


def generate_island_mat(total_size, mig):
    mig_mat = ''
    for x in range(1, total_size + 1):
        for y in range(1, total_size + 1):
            if (x == y):
                mig_mat += '0 '
            else:
                mig_mat += '!!!' + str(mig) + '!!! '
        mig_mat += "\r\n"
    return mig_mat


def generate_null_mat(total_size):
    null_mat = ''
    for x in range(1, total_size + 1):
        for y in range(1, total_size + 1):
            null_mat += '0 '
        null_mat += '\r\n'
    return null_mat


def generate_join_events(t, total_size, join_size, orig_size):
    events = ''
    for i in range(1, total_size - 1):
        events += str(t) + ' ' + str(i) + ' 0 1 1 0 1\r\n'
    events += str(t) + ' ' + str(total_size - 1) + ' 0 1 ' + str(1.0 * total_size * join_size / orig_size) + ' 0 1\r\n'
    return events


def no_processor(in_string):
    return in_string


def process_text(in_string, out_file_prefix, para_list, curr_values,
                 specific_processor):
    text = specific_processor(in_string)
    return process_para(text, out_file_prefix, para_list, [])


# def prepare_dir():
#    try:
#        mkdir(sep.join([Config.dataDir, 'SimCoal'])) # Should exist, but...
#    except OSError:
#        pass # Its ok if already exists
#    try:
#        mkdir(sep.join([Config.dataDir, 'SimCoal', 'runs']))
#    except OSError:
#        pass # Its ok if already exists


# sep is because of jython
def generate_model(par_stream, out_prefix, params,
                   specific_processor=no_processor, out_dir='.'):
    # prepare_dir()
    text = par_stream.read()
    out_file_prefix = sep.join([out_dir, out_prefix])
    return process_text(text, out_file_prefix, params, [], specific_processor)


def get_demography_template(stream, model, tp_dir=None):
    """Gets a demograpy template.

    Most probably this model needs to be sent to GenCases.

    - stream - Writable stream.
    - param  - Template file.
    - tp_dir - Directory where to find the template, if None
               use an internal template
    """
    if tp_dir is None:
        # Internal Template
        filename = sep.join([builtin_tpl_dir, model + '.par'])
    else:
        # External template
        filename = sep.join([tp_dir, model + '.par'])
    with open(filename, 'r') as f:
        l = f.readline()
        while l != '':
            stream.write(l)
            l = f.readline()


def _gen_loci(stream, loci):
    stream.write('//Number of contiguous linkage blocks in chromosome\n')
    stream.write(str(len(loci)) + '\n')
    stream.write('//Per Block: Data type, No. of loci, Recombination rate to the right-side locus, plus optional parameters\n')
    for locus in loci:
        stream.write(' '.join([locus[0]] +
            [str(x) for x in list(locus[1])]) + '\n')


def get_chr_template(stream, chrs):
    """Writes a Simcoal2 loci template part.

    stream - Writable stream.
    chr    - Chromosome list.

    Current loci list:

          - [(chr_repeats,[(marker, (params))])]

              - chr_repeats --> Number of chromosome repeats
              - marker  --> 'SNP', 'DNA', 'RFLP', 'MICROSAT'
              - params  --> Simcoal2 parameters for markers (list of floats
                or ints - if to be processed by generate_model)
    """
    num_chrs = reduce(lambda x, y: x + y[0], chrs, 0)
    stream.write('//Number of independent (unlinked) chromosomes, and "chromosome structure" flag:  0 for identical structure across chromosomes, and  1 for different structures on different chromosomes.\n')
    if len(chrs) > 1 or num_chrs == 1:
        stream.write(str(num_chrs) + ' 1\n')
    else:
        stream.write(str(num_chrs) + ' 0\n')
    for chr in chrs:
        repeats = chr[0]
        loci = chr[1]
        if len(chrs) == 1:
            _gen_loci(stream, loci)
        else:
            for i in range(repeats):
                _gen_loci(stream, loci)


def generate_simcoal_from_template(model, chrs, params, out_dir='.', tp_dir=None):
    """Writes a complete SimCoal2 template file.

    This joins together get_demography_template and get_chr_template,
    which are feed into generate_model
    Please check the three functions for parameters (model from
    get_demography_template, chrs from get_chr_template and
    params from generate_model).
    """
    with open(out_dir + sep + 'tmp.par', 'w') as stream:
        get_demography_template(stream, model, tp_dir)
        get_chr_template(stream, chrs)
    # with open(out_dir + sep + 'tmp.par', 'r') as par_stream:
        # print par_stream.read()
    with open(out_dir + sep + 'tmp.par', 'r') as par_stream:
        generate_model(par_stream, model, params, out_dir=out_dir)