import re
from typing import Union

from deep_phospho.proteomics_utils.constants.enzyme import Enzyme
from deep_phospho.proteomics_utils import rapid_kit as rk


class TED(object):
    def __init__(self, miss_cleavage=(0, 1, 2), min_len=7, max_len=33, enzyme='Trypsin', return_type='seq', extend_n=False):
        """
        TODO exclude some unusual aa if param assigned
        Theoretical Enzyme Digestion -> TED
        :param miss_cleavage: this can be int or tuple, while it will be converted into tuple when use
        :param min_len:
        :param max_len:
        :param enzyme: Enzyme name or a regular expression to define the digestion rules. Currently supported enzymes are trypsin and lysC
        :param return_type: 'seq' or 'site_seq'
        :param extend_n: False or None or int. Nothing to do with the default False, and the n AAs before and after the seq will be returned if int assigned
        """
        self._enzyme = Enzyme()
        self._mc = self._parse_mc(miss_cleavage)
        # TODO Add property for length (min len 7 for default and the func will be able to parse both tuple or int)
        self._min_len = min_len
        self._max_len = max_len
        self._enzyme_names, self._enzyme_rules = self._parse_enzyme(enzyme)
        self._return_type = self._parse_return_type(return_type)
        self._extend_n = self._parse_extend_n(extend_n)

    @staticmethod
    def _parse_mc(mc):
        if isinstance(mc, (tuple, list)):
            pass
        elif isinstance(mc, int):
            mc = (mc, )
        else:
            try:
                mc = (int(mc), )
            except TypeError:
                raise TypeError('Miss cleavage shoule be int or tuple of int')
        return mc

    def get_mc(self):
        return self._mc

    def set_mc(self, mc):
        self._mc = self._parse_mc(mc)

    mc = property(get_mc, set_mc, doc='''Miss cleavage for enzyme digestion''')

    def __find_enzyme(self, enzyme, enzyme_names, enzyme_rules):
        if isinstance(enzyme, str):
            if enzyme not in self._enzyme.AllEnzymes:
                print(f'The input enzyme has no pre-defined digestion rule, the enzyme now used is: {enzyme}\n.'
                      f'This input will be regarded as a regular expression.')
                enzyme_rules.append(enzyme)
            else:
                enzyme_names.append(enzyme)
                enzyme_rules.append(self._enzyme.Enzymes[enzyme]['RE'])
        else:
            raise ValueError(f'The input enzyme {enzyme} is not a string')
        return enzyme_names, enzyme_rules

    def _parse_enzyme(self, enzyme):
        enzyme_names = []
        enzyme_rules = []
        if isinstance(enzyme, str):
            enzyme = (enzyme, )
        elif isinstance(enzyme, (list, tuple, set)):
            pass
        else:
            raise ValueError(f'The input enzyme can not be parsed: {enzyme}')
        for each_enzyme in enzyme:
            enzyme_names, enzyme_rules = self.__find_enzyme(each_enzyme, enzyme_names, enzyme_rules)
        return enzyme_names, enzyme_rules

    def get_enzyme(self):
        return self._enzyme_names, self._enzyme_rules

    def set_enzyme(self, enzyme):
        self._enzyme_names, self._enzyme_rules = self._parse_enzyme(enzyme)

    enzyme = property(get_enzyme, set_enzyme, doc='''Enzyme used for digestion''')

    @staticmethod
    def _parse_return_type(return_type: str):
        if return_type not in ['seq', 'site_seq']:
            raise TypeError(f'The input of return_type should be \'seq\' or \'site_seq\', now: {return_type}')
        return return_type

    def get_return_type(self):
        return self._return_type

    def set_return_type(self, return_type: str):
        self._return_type = self._parse_return_type(return_type)

    return_type = property(get_return_type, set_return_type, doc='''Return type can be seq or site_seq.
    If seq: A list of seq will be returned. ['ADEFHK', 'PQEDAK' , ...]
    If site_seq: A list of site and seq will be returned. [(0, 'ADEFHK'), (12, 'PQEDAK'), ...]''')

    @staticmethod
    def _parse_extend_n(extend_n: Union[bool, None, int]):
        if extend_n is True:
            extend_n = 7
            print(f'The extend_n is set to \'True\' and a conventional sequence window 7 is assigned')
        elif extend_n is None:
            extend_n = False
        elif extend_n is False:
            pass
        elif isinstance(extend_n, int):
            if extend_n == 0:
                extend_n = False
            elif extend_n < 0:
                raise ValueError
            else:
                pass
        else:
            raise TypeError(f'The input of extend_n should be False or None or int, now: {extend_n} with a type {type(extend_n)}')
        return extend_n

    def get_extend_n(self):
        return self._extend_n

    def set_extend_n(self, extend_n: Union[bool, None, int]):
        self._extend_n = self._parse_extend_n(extend_n)

    extend_n = property(get_extend_n, set_extend_n, doc='''Extended AA number can be False or None or int.
    Nothing to do with the default False or None is assigned.
    If int: the n AAs before and after the seq will be returned.
    If True: the n will be set to 7 as a conventional sequence window''')

    def __call__(self, seq, add_info=None):
        """
        考虑到之后可能有多种酶同时加入的情况，以及需要前后 n 个 AA 的情况，这里改成对每个 seq 分别用所有 digestion rule 拿到可以切的位点，然后再去组装
            这样可以简化正则的匹配规则同时减少处理步骤
        """
        seq = seq.replace('\n', '').replace(' ', '')
        seq_len = len(seq)

        cleavage_pos = rk.sum_list([[_.end() for _ in re.finditer(rule, seq)] for rule in self._enzyme_rules]) + [0, seq_len]
        cleavage_pos = sorted(set(cleavage_pos))

        cleavage_pos_num = len(cleavage_pos)
        pos_comb = []
        for idx, pos in enumerate(cleavage_pos):
            for mc in self._mc:
                end_pos_idx = idx + mc + 1
                if end_pos_idx >= cleavage_pos_num:
                    continue
                else:
                    pos_comb.append((pos, cleavage_pos[end_pos_idx]))

        compliant_seq = []
        for start_idx, end_pos in pos_comb:
            one_seq = seq[start_idx: end_pos]
            seq_len = len(one_seq)
            if seq_len < self._min_len or seq_len > self._max_len:
                continue
            else:
                if self._return_type == 'seq':
                    one_data = (one_seq, )
                elif self._return_type == 'site_seq':
                    one_data = (start_idx, one_seq)
                else:
                    raise ValueError
                if self._extend_n:
                    if start_idx < self._extend_n:
                        prev_seq = '_' * (self._extend_n - start_idx) + seq[: start_idx]
                    else:
                        prev_seq = seq[start_idx - self._extend_n: start_idx]
                    back_seq = seq[end_pos: end_pos + self._extend_n]
                    if len(back_seq) < self._extend_n:
                        back_seq = back_seq + '_' * (self._extend_n - len(back_seq))
                    one_data = (*one_data, prev_seq, back_seq)
                if add_info is not None:
                    if not isinstance(add_info, (tuple, list)):
                        add_info = (add_info, )
                    one_data = (*one_data, *add_info)
                if len(one_data) == 1:
                    one_data = one_data[0]
                compliant_seq.append(one_data)
        return compliant_seq

d6506ab28cee890007bab3070e3de6011b786afd
<mask token>


class TED(object):
    <mask token>
    <mask token>

    def get_mc(self):
        return self._mc
    <mask token>
    <mask token>

    def __find_enzyme(self, enzyme, enzyme_names, enzyme_rules):
        if isinstance(enzyme, str):
            if enzyme not in self._enzyme.AllEnzymes:
                print(
                    f"""The input enzyme has no pre-defined digestion rule, the enzyme now used is: {enzyme}
.This input will be regarded as a regular expression."""
                    )
                enzyme_rules.append(enzyme)
            else:
                enzyme_names.append(enzyme)
                enzyme_rules.append(self._enzyme.Enzymes[enzyme]['RE'])
        else:
            raise ValueError(f'The input enzyme {enzyme} is not a string')
        return enzyme_names, enzyme_rules

    def _parse_enzyme(self, enzyme):
        enzyme_names = []
        enzyme_rules = []
        if isinstance(enzyme, str):
            enzyme = enzyme,
        elif isinstance(enzyme, (list, tuple, set)):
            pass
        else:
            raise ValueError(f'The input enzyme can not be parsed: {enzyme}')
        for each_enzyme in enzyme:
            enzyme_names, enzyme_rules = self.__find_enzyme(each_enzyme,
                enzyme_names, enzyme_rules)
        return enzyme_names, enzyme_rules

    def get_enzyme(self):
        return self._enzyme_names, self._enzyme_rules

    def set_enzyme(self, enzyme):
        self._enzyme_names, self._enzyme_rules = self._parse_enzyme(enzyme)
    <mask token>

    @staticmethod
    def _parse_return_type(return_type: str):
        if return_type not in ['seq', 'site_seq']:
            raise TypeError(
                f"The input of return_type should be 'seq' or 'site_seq', now: {return_type}"
                )
        return return_type
    <mask token>

    def set_return_type(self, return_type: str):
        self._return_type = self._parse_return_type(return_type)
    <mask token>
    <mask token>

    def get_extend_n(self):
        return self._extend_n

    def set_extend_n(self, extend_n: Union[bool, None, int]):
        self._extend_n = self._parse_extend_n(extend_n)
    <mask token>

    def __call__(self, seq, add_info=None):
        """
        考虑到之后可能有多种酶同时加入的情况，以及需要前后 n 个 AA 的情况，这里改成对每个 seq 分别用所有 digestion rule 拿到可以切的位点，然后再去组装
            这样可以简化正则的匹配规则同时减少处理步骤
        """
        seq = seq.replace('\n', '').replace(' ', '')
        seq_len = len(seq)
        cleavage_pos = rk.sum_list([[_.end() for _ in re.finditer(rule, seq
            )] for rule in self._enzyme_rules]) + [0, seq_len]
        cleavage_pos = sorted(set(cleavage_pos))
        cleavage_pos_num = len(cleavage_pos)
        pos_comb = []
        for idx, pos in enumerate(cleavage_pos):
            for mc in self._mc:
                end_pos_idx = idx + mc + 1
                if end_pos_idx >= cleavage_pos_num:
                    continue
                else:
                    pos_comb.append((pos, cleavage_pos[end_pos_idx]))
        compliant_seq = []
        for start_idx, end_pos in pos_comb:
            one_seq = seq[start_idx:end_pos]
            seq_len = len(one_seq)
            if seq_len < self._min_len or seq_len > self._max_len:
                continue
            else:
                if self._return_type == 'seq':
                    one_data = one_seq,
                elif self._return_type == 'site_seq':
                    one_data = start_idx, one_seq
                else:
                    raise ValueError
                if self._extend_n:
                    if start_idx < self._extend_n:
                        prev_seq = '_' * (self._extend_n - start_idx) + seq[:
                            start_idx]
                    else:
                        prev_seq = seq[start_idx - self._extend_n:start_idx]
                    back_seq = seq[end_pos:end_pos + self._extend_n]
                    if len(back_seq) < self._extend_n:
                        back_seq = back_seq + '_' * (self._extend_n - len(
                            back_seq))
                    one_data = *one_data, prev_seq, back_seq
                if add_info is not None:
                    if not isinstance(add_info, (tuple, list)):
                        add_info = add_info,
                    one_data = *one_data, *add_info
                if len(one_data) == 1:
                    one_data = one_data[0]
                compliant_seq.append(one_data)
        return compliant_seq

<mask token>


class TED(object):
    <mask token>
    <mask token>

    def get_mc(self):
        return self._mc
    <mask token>
    <mask token>

    def __find_enzyme(self, enzyme, enzyme_names, enzyme_rules):
        if isinstance(enzyme, str):
            if enzyme not in self._enzyme.AllEnzymes:
                print(
                    f"""The input enzyme has no pre-defined digestion rule, the enzyme now used is: {enzyme}
.This input will be regarded as a regular expression."""
                    )
                enzyme_rules.append(enzyme)
            else:
                enzyme_names.append(enzyme)
                enzyme_rules.append(self._enzyme.Enzymes[enzyme]['RE'])
        else:
            raise ValueError(f'The input enzyme {enzyme} is not a string')
        return enzyme_names, enzyme_rules

    def _parse_enzyme(self, enzyme):
        enzyme_names = []
        enzyme_rules = []
        if isinstance(enzyme, str):
            enzyme = enzyme,
        elif isinstance(enzyme, (list, tuple, set)):
            pass
        else:
            raise ValueError(f'The input enzyme can not be parsed: {enzyme}')
        for each_enzyme in enzyme:
            enzyme_names, enzyme_rules = self.__find_enzyme(each_enzyme,
                enzyme_names, enzyme_rules)
        return enzyme_names, enzyme_rules

    def get_enzyme(self):
        return self._enzyme_names, self._enzyme_rules

    def set_enzyme(self, enzyme):
        self._enzyme_names, self._enzyme_rules = self._parse_enzyme(enzyme)
    <mask token>

    @staticmethod
    def _parse_return_type(return_type: str):
        if return_type not in ['seq', 'site_seq']:
            raise TypeError(
                f"The input of return_type should be 'seq' or 'site_seq', now: {return_type}"
                )
        return return_type

    def get_return_type(self):
        return self._return_type

    def set_return_type(self, return_type: str):
        self._return_type = self._parse_return_type(return_type)
    <mask token>
    <mask token>

    def get_extend_n(self):
        return self._extend_n

    def set_extend_n(self, extend_n: Union[bool, None, int]):
        self._extend_n = self._parse_extend_n(extend_n)
    <mask token>

    def __call__(self, seq, add_info=None):
        """
        考虑到之后可能有多种酶同时加入的情况，以及需要前后 n 个 AA 的情况，这里改成对每个 seq 分别用所有 digestion rule 拿到可以切的位点，然后再去组装
            这样可以简化正则的匹配规则同时减少处理步骤
        """
        seq = seq.replace('\n', '').replace(' ', '')
        seq_len = len(seq)
        cleavage_pos = rk.sum_list([[_.end() for _ in re.finditer(rule, seq
            )] for rule in self._enzyme_rules]) + [0, seq_len]
        cleavage_pos = sorted(set(cleavage_pos))
        cleavage_pos_num = len(cleavage_pos)
        pos_comb = []
        for idx, pos in enumerate(cleavage_pos):
            for mc in self._mc:
                end_pos_idx = idx + mc + 1
                if end_pos_idx >= cleavage_pos_num:
                    continue
                else:
                    pos_comb.append((pos, cleavage_pos[end_pos_idx]))
        compliant_seq = []
        for start_idx, end_pos in pos_comb:
            one_seq = seq[start_idx:end_pos]
            seq_len = len(one_seq)
            if seq_len < self._min_len or seq_len > self._max_len:
                continue
            else:
                if self._return_type == 'seq':
                    one_data = one_seq,
                elif self._return_type == 'site_seq':
                    one_data = start_idx, one_seq
                else:
                    raise ValueError
                if self._extend_n:
                    if start_idx < self._extend_n:
                        prev_seq = '_' * (self._extend_n - start_idx) + seq[:
                            start_idx]
                    else:
                        prev_seq = seq[start_idx - self._extend_n:start_idx]
                    back_seq = seq[end_pos:end_pos + self._extend_n]
                    if len(back_seq) < self._extend_n:
                        back_seq = back_seq + '_' * (self._extend_n - len(
                            back_seq))
                    one_data = *one_data, prev_seq, back_seq
                if add_info is not None:
                    if not isinstance(add_info, (tuple, list)):
                        add_info = add_info,
                    one_data = *one_data, *add_info
                if len(one_data) == 1:
                    one_data = one_data[0]
                compliant_seq.append(one_data)
        return compliant_seq

<mask token>


class TED(object):

    def __init__(self, miss_cleavage=(0, 1, 2), min_len=7, max_len=33,
        enzyme='Trypsin', return_type='seq', extend_n=False):
        """
        TODO exclude some unusual aa if param assigned
        Theoretical Enzyme Digestion -> TED
        :param miss_cleavage: this can be int or tuple, while it will be converted into tuple when use
        :param min_len:
        :param max_len:
        :param enzyme: Enzyme name or a regular expression to define the digestion rules. Currently supported enzymes are trypsin and lysC
        :param return_type: 'seq' or 'site_seq'
        :param extend_n: False or None or int. Nothing to do with the default False, and the n AAs before and after the seq will be returned if int assigned
        """
        self._enzyme = Enzyme()
        self._mc = self._parse_mc(miss_cleavage)
        self._min_len = min_len
        self._max_len = max_len
        self._enzyme_names, self._enzyme_rules = self._parse_enzyme(enzyme)
        self._return_type = self._parse_return_type(return_type)
        self._extend_n = self._parse_extend_n(extend_n)

    @staticmethod
    def _parse_mc(mc):
        if isinstance(mc, (tuple, list)):
            pass
        elif isinstance(mc, int):
            mc = mc,
        else:
            try:
                mc = int(mc),
            except TypeError:
                raise TypeError('Miss cleavage shoule be int or tuple of int')
        return mc

    def get_mc(self):
        return self._mc

    def set_mc(self, mc):
        self._mc = self._parse_mc(mc)
    mc = property(get_mc, set_mc, doc='Miss cleavage for enzyme digestion')

    def __find_enzyme(self, enzyme, enzyme_names, enzyme_rules):
        if isinstance(enzyme, str):
            if enzyme not in self._enzyme.AllEnzymes:
                print(
                    f"""The input enzyme has no pre-defined digestion rule, the enzyme now used is: {enzyme}
.This input will be regarded as a regular expression."""
                    )
                enzyme_rules.append(enzyme)
            else:
                enzyme_names.append(enzyme)
                enzyme_rules.append(self._enzyme.Enzymes[enzyme]['RE'])
        else:
            raise ValueError(f'The input enzyme {enzyme} is not a string')
        return enzyme_names, enzyme_rules

    def _parse_enzyme(self, enzyme):
        enzyme_names = []
        enzyme_rules = []
        if isinstance(enzyme, str):
            enzyme = enzyme,
        elif isinstance(enzyme, (list, tuple, set)):
            pass
        else:
            raise ValueError(f'The input enzyme can not be parsed: {enzyme}')
        for each_enzyme in enzyme:
            enzyme_names, enzyme_rules = self.__find_enzyme(each_enzyme,
                enzyme_names, enzyme_rules)
        return enzyme_names, enzyme_rules

    def get_enzyme(self):
        return self._enzyme_names, self._enzyme_rules

    def set_enzyme(self, enzyme):
        self._enzyme_names, self._enzyme_rules = self._parse_enzyme(enzyme)
    enzyme = property(get_enzyme, set_enzyme, doc='Enzyme used for digestion')

    @staticmethod
    def _parse_return_type(return_type: str):
        if return_type not in ['seq', 'site_seq']:
            raise TypeError(
                f"The input of return_type should be 'seq' or 'site_seq', now: {return_type}"
                )
        return return_type

    def get_return_type(self):
        return self._return_type

    def set_return_type(self, return_type: str):
        self._return_type = self._parse_return_type(return_type)
    return_type = property(get_return_type, set_return_type, doc=
        """Return type can be seq or site_seq.
    If seq: A list of seq will be returned. ['ADEFHK', 'PQEDAK' , ...]
    If site_seq: A list of site and seq will be returned. [(0, 'ADEFHK'), (12, 'PQEDAK'), ...]"""
        )

    @staticmethod
    def _parse_extend_n(extend_n: Union[bool, None, int]):
        if extend_n is True:
            extend_n = 7
            print(
                f"The extend_n is set to 'True' and a conventional sequence window 7 is assigned"
                )
        elif extend_n is None:
            extend_n = False
        elif extend_n is False:
            pass
        elif isinstance(extend_n, int):
            if extend_n == 0:
                extend_n = False
            elif extend_n < 0:
                raise ValueError
            else:
                pass
        else:
            raise TypeError(
                f'The input of extend_n should be False or None or int, now: {extend_n} with a type {type(extend_n)}'
                )
        return extend_n

    def get_extend_n(self):
        return self._extend_n

    def set_extend_n(self, extend_n: Union[bool, None, int]):
        self._extend_n = self._parse_extend_n(extend_n)
    extend_n = property(get_extend_n, set_extend_n, doc=
        """Extended AA number can be False or None or int.
    Nothing to do with the default False or None is assigned.
    If int: the n AAs before and after the seq will be returned.
    If True: the n will be set to 7 as a conventional sequence window"""
        )

    def __call__(self, seq, add_info=None):
        """
        考虑到之后可能有多种酶同时加入的情况，以及需要前后 n 个 AA 的情况，这里改成对每个 seq 分别用所有 digestion rule 拿到可以切的位点，然后再去组装
            这样可以简化正则的匹配规则同时减少处理步骤
        """
        seq = seq.replace('\n', '').replace(' ', '')
        seq_len = len(seq)
        cleavage_pos = rk.sum_list([[_.end() for _ in re.finditer(rule, seq
            )] for rule in self._enzyme_rules]) + [0, seq_len]
        cleavage_pos = sorted(set(cleavage_pos))
        cleavage_pos_num = len(cleavage_pos)
        pos_comb = []
        for idx, pos in enumerate(cleavage_pos):
            for mc in self._mc:
                end_pos_idx = idx + mc + 1
                if end_pos_idx >= cleavage_pos_num:
                    continue
                else:
                    pos_comb.append((pos, cleavage_pos[end_pos_idx]))
        compliant_seq = []
        for start_idx, end_pos in pos_comb:
            one_seq = seq[start_idx:end_pos]
            seq_len = len(one_seq)
            if seq_len < self._min_len or seq_len > self._max_len:
                continue
            else:
                if self._return_type == 'seq':
                    one_data = one_seq,
                elif self._return_type == 'site_seq':
                    one_data = start_idx, one_seq
                else:
                    raise ValueError
                if self._extend_n:
                    if start_idx < self._extend_n:
                        prev_seq = '_' * (self._extend_n - start_idx) + seq[:
                            start_idx]
                    else:
                        prev_seq = seq[start_idx - self._extend_n:start_idx]
                    back_seq = seq[end_pos:end_pos + self._extend_n]
                    if len(back_seq) < self._extend_n:
                        back_seq = back_seq + '_' * (self._extend_n - len(
                            back_seq))
                    one_data = *one_data, prev_seq, back_seq
                if add_info is not None:
                    if not isinstance(add_info, (tuple, list)):
                        add_info = add_info,
                    one_data = *one_data, *add_info
                if len(one_data) == 1:
                    one_data = one_data[0]
                compliant_seq.append(one_data)
        return compliant_seq

import re
from typing import Union
from deep_phospho.proteomics_utils.constants.enzyme import Enzyme
from deep_phospho.proteomics_utils import rapid_kit as rk


class TED(object):

    def __init__(self, miss_cleavage=(0, 1, 2), min_len=7, max_len=33,
        enzyme='Trypsin', return_type='seq', extend_n=False):
        """
        TODO exclude some unusual aa if param assigned
        Theoretical Enzyme Digestion -> TED
        :param miss_cleavage: this can be int or tuple, while it will be converted into tuple when use
        :param min_len:
        :param max_len:
        :param enzyme: Enzyme name or a regular expression to define the digestion rules. Currently supported enzymes are trypsin and lysC
        :param return_type: 'seq' or 'site_seq'
        :param extend_n: False or None or int. Nothing to do with the default False, and the n AAs before and after the seq will be returned if int assigned
        """
        self._enzyme = Enzyme()
        self._mc = self._parse_mc(miss_cleavage)
        self._min_len = min_len
        self._max_len = max_len
        self._enzyme_names, self._enzyme_rules = self._parse_enzyme(enzyme)
        self._return_type = self._parse_return_type(return_type)
        self._extend_n = self._parse_extend_n(extend_n)

    @staticmethod
    def _parse_mc(mc):
        if isinstance(mc, (tuple, list)):
            pass
        elif isinstance(mc, int):
            mc = mc,
        else:
            try:
                mc = int(mc),
            except TypeError:
                raise TypeError('Miss cleavage shoule be int or tuple of int')
        return mc

    def get_mc(self):
        return self._mc

    def set_mc(self, mc):
        self._mc = self._parse_mc(mc)
    mc = property(get_mc, set_mc, doc='Miss cleavage for enzyme digestion')

    def __find_enzyme(self, enzyme, enzyme_names, enzyme_rules):
        if isinstance(enzyme, str):
            if enzyme not in self._enzyme.AllEnzymes:
                print(
                    f"""The input enzyme has no pre-defined digestion rule, the enzyme now used is: {enzyme}
.This input will be regarded as a regular expression."""
                    )
                enzyme_rules.append(enzyme)
            else:
                enzyme_names.append(enzyme)
                enzyme_rules.append(self._enzyme.Enzymes[enzyme]['RE'])
        else:
            raise ValueError(f'The input enzyme {enzyme} is not a string')
        return enzyme_names, enzyme_rules

    def _parse_enzyme(self, enzyme):
        enzyme_names = []
        enzyme_rules = []
        if isinstance(enzyme, str):
            enzyme = enzyme,
        elif isinstance(enzyme, (list, tuple, set)):
            pass
        else:
            raise ValueError(f'The input enzyme can not be parsed: {enzyme}')
        for each_enzyme in enzyme:
            enzyme_names, enzyme_rules = self.__find_enzyme(each_enzyme,
                enzyme_names, enzyme_rules)
        return enzyme_names, enzyme_rules

    def get_enzyme(self):
        return self._enzyme_names, self._enzyme_rules

    def set_enzyme(self, enzyme):
        self._enzyme_names, self._enzyme_rules = self._parse_enzyme(enzyme)
    enzyme = property(get_enzyme, set_enzyme, doc='Enzyme used for digestion')

    @staticmethod
    def _parse_return_type(return_type: str):
        if return_type not in ['seq', 'site_seq']:
            raise TypeError(
                f"The input of return_type should be 'seq' or 'site_seq', now: {return_type}"
                )
        return return_type

    def get_return_type(self):
        return self._return_type

    def set_return_type(self, return_type: str):
        self._return_type = self._parse_return_type(return_type)
    return_type = property(get_return_type, set_return_type, doc=
        """Return type can be seq or site_seq.
    If seq: A list of seq will be returned. ['ADEFHK', 'PQEDAK' , ...]
    If site_seq: A list of site and seq will be returned. [(0, 'ADEFHK'), (12, 'PQEDAK'), ...]"""
        )

    @staticmethod
    def _parse_extend_n(extend_n: Union[bool, None, int]):
        if extend_n is True:
            extend_n = 7
            print(
                f"The extend_n is set to 'True' and a conventional sequence window 7 is assigned"
                )
        elif extend_n is None:
            extend_n = False
        elif extend_n is False:
            pass
        elif isinstance(extend_n, int):
            if extend_n == 0:
                extend_n = False
            elif extend_n < 0:
                raise ValueError
            else:
                pass
        else:
            raise TypeError(
                f'The input of extend_n should be False or None or int, now: {extend_n} with a type {type(extend_n)}'
                )
        return extend_n

    def get_extend_n(self):
        return self._extend_n

    def set_extend_n(self, extend_n: Union[bool, None, int]):
        self._extend_n = self._parse_extend_n(extend_n)
    extend_n = property(get_extend_n, set_extend_n, doc=
        """Extended AA number can be False or None or int.
    Nothing to do with the default False or None is assigned.
    If int: the n AAs before and after the seq will be returned.
    If True: the n will be set to 7 as a conventional sequence window"""
        )

    def __call__(self, seq, add_info=None):
        """
        考虑到之后可能有多种酶同时加入的情况，以及需要前后 n 个 AA 的情况，这里改成对每个 seq 分别用所有 digestion rule 拿到可以切的位点，然后再去组装
            这样可以简化正则的匹配规则同时减少处理步骤
        """
        seq = seq.replace('\n', '').replace(' ', '')
        seq_len = len(seq)
        cleavage_pos = rk.sum_list([[_.end() for _ in re.finditer(rule, seq
            )] for rule in self._enzyme_rules]) + [0, seq_len]
        cleavage_pos = sorted(set(cleavage_pos))
        cleavage_pos_num = len(cleavage_pos)
        pos_comb = []
        for idx, pos in enumerate(cleavage_pos):
            for mc in self._mc:
                end_pos_idx = idx + mc + 1
                if end_pos_idx >= cleavage_pos_num:
                    continue
                else:
                    pos_comb.append((pos, cleavage_pos[end_pos_idx]))
        compliant_seq = []
        for start_idx, end_pos in pos_comb:
            one_seq = seq[start_idx:end_pos]
            seq_len = len(one_seq)
            if seq_len < self._min_len or seq_len > self._max_len:
                continue
            else:
                if self._return_type == 'seq':
                    one_data = one_seq,
                elif self._return_type == 'site_seq':
                    one_data = start_idx, one_seq
                else:
                    raise ValueError
                if self._extend_n:
                    if start_idx < self._extend_n:
                        prev_seq = '_' * (self._extend_n - start_idx) + seq[:
                            start_idx]
                    else:
                        prev_seq = seq[start_idx - self._extend_n:start_idx]
                    back_seq = seq[end_pos:end_pos + self._extend_n]
                    if len(back_seq) < self._extend_n:
                        back_seq = back_seq + '_' * (self._extend_n - len(
                            back_seq))
                    one_data = *one_data, prev_seq, back_seq
                if add_info is not None:
                    if not isinstance(add_info, (tuple, list)):
                        add_info = add_info,
                    one_data = *one_data, *add_info
                if len(one_data) == 1:
                    one_data = one_data[0]
                compliant_seq.append(one_data)
        return compliant_seq

import re
from typing import Union

from deep_phospho.proteomics_utils.constants.enzyme import Enzyme
from deep_phospho.proteomics_utils import rapid_kit as rk


class TED(object):
    def __init__(self, miss_cleavage=(0, 1, 2), min_len=7, max_len=33, enzyme='Trypsin', return_type='seq', extend_n=False):
        """
        TODO exclude some unusual aa if param assigned
        Theoretical Enzyme Digestion -> TED
        :param miss_cleavage: this can be int or tuple, while it will be converted into tuple when use
        :param min_len:
        :param max_len:
        :param enzyme: Enzyme name or a regular expression to define the digestion rules. Currently supported enzymes are trypsin and lysC
        :param return_type: 'seq' or 'site_seq'
        :param extend_n: False or None or int. Nothing to do with the default False, and the n AAs before and after the seq will be returned if int assigned
        """
        self._enzyme = Enzyme()
        self._mc = self._parse_mc(miss_cleavage)
        # TODO Add property for length (min len 7 for default and the func will be able to parse both tuple or int)
        self._min_len = min_len
        self._max_len = max_len
        self._enzyme_names, self._enzyme_rules = self._parse_enzyme(enzyme)
        self._return_type = self._parse_return_type(return_type)
        self._extend_n = self._parse_extend_n(extend_n)

    @staticmethod
    def _parse_mc(mc):
        if isinstance(mc, (tuple, list)):
            pass
        elif isinstance(mc, int):
            mc = (mc, )
        else:
            try:
                mc = (int(mc), )
            except TypeError:
                raise TypeError('Miss cleavage shoule be int or tuple of int')
        return mc

    def get_mc(self):
        return self._mc

    def set_mc(self, mc):
        self._mc = self._parse_mc(mc)

    mc = property(get_mc, set_mc, doc='''Miss cleavage for enzyme digestion''')

    def __find_enzyme(self, enzyme, enzyme_names, enzyme_rules):
        if isinstance(enzyme, str):
            if enzyme not in self._enzyme.AllEnzymes:
                print(f'The input enzyme has no pre-defined digestion rule, the enzyme now used is: {enzyme}\n.'
                      f'This input will be regarded as a regular expression.')
                enzyme_rules.append(enzyme)
            else:
                enzyme_names.append(enzyme)
                enzyme_rules.append(self._enzyme.Enzymes[enzyme]['RE'])
        else:
            raise ValueError(f'The input enzyme {enzyme} is not a string')
        return enzyme_names, enzyme_rules

    def _parse_enzyme(self, enzyme):
        enzyme_names = []
        enzyme_rules = []
        if isinstance(enzyme, str):
            enzyme = (enzyme, )
        elif isinstance(enzyme, (list, tuple, set)):
            pass
        else:
            raise ValueError(f'The input enzyme can not be parsed: {enzyme}')
        for each_enzyme in enzyme:
            enzyme_names, enzyme_rules = self.__find_enzyme(each_enzyme, enzyme_names, enzyme_rules)
        return enzyme_names, enzyme_rules

    def get_enzyme(self):
        return self._enzyme_names, self._enzyme_rules

    def set_enzyme(self, enzyme):
        self._enzyme_names, self._enzyme_rules = self._parse_enzyme(enzyme)

    enzyme = property(get_enzyme, set_enzyme, doc='''Enzyme used for digestion''')

    @staticmethod
    def _parse_return_type(return_type: str):
        if return_type not in ['seq', 'site_seq']:
            raise TypeError(f'The input of return_type should be \'seq\' or \'site_seq\', now: {return_type}')
        return return_type

    def get_return_type(self):
        return self._return_type

    def set_return_type(self, return_type: str):
        self._return_type = self._parse_return_type(return_type)

    return_type = property(get_return_type, set_return_type, doc='''Return type can be seq or site_seq.
    If seq: A list of seq will be returned. ['ADEFHK', 'PQEDAK' , ...]
    If site_seq: A list of site and seq will be returned. [(0, 'ADEFHK'), (12, 'PQEDAK'), ...]''')

    @staticmethod
    def _parse_extend_n(extend_n: Union[bool, None, int]):
        if extend_n is True:
            extend_n = 7
            print(f'The extend_n is set to \'True\' and a conventional sequence window 7 is assigned')
        elif extend_n is None:
            extend_n = False
        elif extend_n is False:
            pass
        elif isinstance(extend_n, int):
            if extend_n == 0:
                extend_n = False
            elif extend_n < 0:
                raise ValueError
            else:
                pass
        else:
            raise TypeError(f'The input of extend_n should be False or None or int, now: {extend_n} with a type {type(extend_n)}')
        return extend_n

    def get_extend_n(self):
        return self._extend_n

    def set_extend_n(self, extend_n: Union[bool, None, int]):
        self._extend_n = self._parse_extend_n(extend_n)

    extend_n = property(get_extend_n, set_extend_n, doc='''Extended AA number can be False or None or int.
    Nothing to do with the default False or None is assigned.
    If int: the n AAs before and after the seq will be returned.
    If True: the n will be set to 7 as a conventional sequence window''')

    def __call__(self, seq, add_info=None):
        """
        考虑到之后可能有多种酶同时加入的情况，以及需要前后 n 个 AA 的情况，这里改成对每个 seq 分别用所有 digestion rule 拿到可以切的位点，然后再去组装
            这样可以简化正则的匹配规则同时减少处理步骤
        """
        seq = seq.replace('\n', '').replace(' ', '')
        seq_len = len(seq)

        cleavage_pos = rk.sum_list([[_.end() for _ in re.finditer(rule, seq)] for rule in self._enzyme_rules]) + [0, seq_len]
        cleavage_pos = sorted(set(cleavage_pos))

        cleavage_pos_num = len(cleavage_pos)
        pos_comb = []
        for idx, pos in enumerate(cleavage_pos):
            for mc in self._mc:
                end_pos_idx = idx + mc + 1
                if end_pos_idx >= cleavage_pos_num:
                    continue
                else:
                    pos_comb.append((pos, cleavage_pos[end_pos_idx]))

        compliant_seq = []
        for start_idx, end_pos in pos_comb:
            one_seq = seq[start_idx: end_pos]
            seq_len = len(one_seq)
            if seq_len < self._min_len or seq_len > self._max_len:
                continue
            else:
                if self._return_type == 'seq':
                    one_data = (one_seq, )
                elif self._return_type == 'site_seq':
                    one_data = (start_idx, one_seq)
                else:
                    raise ValueError
                if self._extend_n:
                    if start_idx < self._extend_n:
                        prev_seq = '_' * (self._extend_n - start_idx) + seq[: start_idx]
                    else:
                        prev_seq = seq[start_idx - self._extend_n: start_idx]
                    back_seq = seq[end_pos: end_pos + self._extend_n]
                    if len(back_seq) < self._extend_n:
                        back_seq = back_seq + '_' * (self._extend_n - len(back_seq))
                    one_data = (*one_data, prev_seq, back_seq)
                if add_info is not None:
                    if not isinstance(add_info, (tuple, list)):
                        add_info = (add_info, )
                    one_data = (*one_data, *add_info)
                if len(one_data) == 1:
                    one_data = one_data[0]
                compliant_seq.append(one_data)
        return compliant_seq
