from typing import Union, Tuple, Optional

from genomics_data_index.storage.model.QueryFeatureHGVS import QueryFeatureHGVS
from genomics_data_index.storage.model.QueryFeatureMutationSPDI import QueryFeatureMutationSPDI


class NucleotideMutationTranslater:

    @classmethod
    def convert_deletion(cls, deletion: Union[str, int]) -> int:
        if isinstance(deletion, str):
            if deletion.isdigit():
                deletion = int(deletion)
            else:
                if not set(deletion).issubset({'A', 'T', 'C', 'G', 'N'}):
                    raise Exception('Deletion must either be an integer or a string with alphabet {A,T,C,G,N}'
                                    f': {deletion}')
                deletion = len(deletion)
        elif isinstance(deletion, int):
            if deletion < 0:
                raise Exception(f'ref=[{deletion}] must be a non-negative integer')
        else:
            raise Exception(f'ref=[{deletion}] must be either a string or a non-negative integer')

        return deletion

    @classmethod
    def from_spdi(cls, spdi: str, convert_deletion=True) -> Tuple[str, int, Union[int, str], str]:
        if spdi is None:
            raise Exception('Cannot parse value spdi=None')

        values = spdi.split(':')
        if len(values) != 4:
            raise Exception(f'Incorrect number of items for spdi=[{spdi}]')
        else:
            position = int(values[1])

            if convert_deletion:
                deletion = cls.convert_deletion(values[2])
            else:
                deletion = values[2]
                if deletion.isdigit():
                    deletion = int(deletion)
                elif deletion == '':
                    raise Exception(f'deletion=[{deletion}] but convert_deletion is False')

            if position < 0:
                raise Exception(f'Position must be non-negative: {position}')

            return str(values[0]), position, deletion, str(values[3])

    @classmethod
    def to_spdi(cls, sequence_name: str, position: int, ref: Union[str, int], alt: str,
                convert_deletion: bool = True) -> str:
        if position < 0:
            raise Exception(f'Position must be non-negative: {position}')

        if convert_deletion:
            ref = cls.convert_deletion(ref)

        return f'{sequence_name}:{position}:{ref}:{alt}'

    @classmethod
    def to_db_feature(cls, feature: QueryFeatureMutationSPDI) -> QueryFeatureMutationSPDI:
        new_id = cls.to_spdi(feature.scope, feature.position, feature.ref, feature.alt)
        return QueryFeatureMutationSPDI(new_id)

    @classmethod
    def to_hgvs_id(cls, sequence_name: str, gene: Optional[str], variant: str) -> Optional[str]:
        return QueryFeatureHGVS.create(sequence_name=sequence_name,
                                       gene=gene,
                                       variant=variant).id
