Controller.py

from UseCases import DnaManager, RnaManager, ProteinManager
import Presenter


def align_helper(seq1, seq2) -> str:
    one = seq1.upper()
    two = seq2.upper()
    mismatches = ''
    if len(one) <= len(two):
        for i in range(len(one)):
            if one[i] != two[i]:
                mismatches += '|'
            else:
                mismatches += ' '
    else:
        for i in range(len(two)):
            if two[i] != one[i]:
                mismatches += '|'
            else:
                mismatches += ' '
    return mismatches


class ProteinSystem:

    _dm: DnaManager()
    _rm: RnaManager()
    _pm: ProteinManager()

    def __init__(self, dm, rm, pm):
        self._dm = dm
        self._rm = rm
        self._pm = pm

    def dna_pairing(self, sequence) -> str:
        """Acts in the Controller method in Clean Architecture to find
        complementary DNA pair of a given DNA sequence.

        :param sequence: DNA sequence input
        :return Complementary DNA sequence"""
        return self._dm.find_dna_pair(sequence)

    def get_mrna(self, sequence) -> str:
        """Acts in the Controller method in Clean Architecture to find
        complementary RNA pair of a given DNA sequence.

        :param sequence: DNA sequence input
        :return Complementary RNA sequence"""
        return self._dm.dna_to_rna_(sequence)

    def get_protein(self, sequence) -> str:
        """Acts in the Controller method in Clean Architecture to find
        the protein chain of a given RNA sequence.

        :param sequence: RNA sequence input
        :return matching protein chain"""
        sequence = sequence.upper()
        if self._dm.dna_to_rna_(sequence) != Presenter.print_invalid():
            mrna = self._dm.dna_to_rna_(sequence)
            return self._rm.rna_to_protein(mrna)
        return Presenter.print_invalid()

    def get_dna(self, sequence) -> str:
        """Acts in the Controller method in Clean Architecture to find
        complementary DNA pair of a given RNA sequence.

        :param sequence: RNA sequence input
        :return Complementary DNA sequence"""
        return self._rm.rna_to_dna_pair(sequence)

    def compare_dna(self, seq1, seq2) -> str:
        if len(seq1) > 70 or len(seq2) > 70:
            return Presenter.print_sequence_max()
        if not self._dm.valid_dna_seq(seq1):
            return Presenter.print_invalid_seq1()
        if not self._dm.valid_dna_seq(seq2):
            return Presenter.print_invalid_seq2()
        return seq1.upper() + '\n' + align_helper(seq1,
                                                  seq2) + '\n' + seq2.upper()

    def compare_rna(self, seq1, seq2) -> str:
        if len(seq1) > 70 or len(seq2) > 70:
            return Presenter.print_sequence_max()
        if not self._rm.valid_rna_seq(seq1):
            return Presenter.print_invalid_seq1()
        if not self._rm.valid_rna_seq(seq2):
            return Presenter.print_invalid_seq2()
        return seq1.upper() + '\n' + align_helper(seq1,
                                                  seq2) + '\n' + seq2.upper()

    def compare_protein(self, seq1, seq2) -> str:
        if len(seq1) > 70 or len(seq2) > 70:
            return Presenter.print_sequence_max()
        if not self._pm.valid_protein_sequence(seq1):
            return Presenter.print_invalid_seq1()
        if not self._pm.valid_protein_sequence(seq2):
            return Presenter.print_invalid_seq2()
        return seq1.upper() + '\n' + align_helper(seq1,
                                                  seq2) + '\n' + seq2.upper()