from numpy import array
from pickle import load
from pandas import read_csv
import os
from BioCAT.src.Combinatorics import multi_thread_shuffling, multi_thread_calculating_scores, make_combine, get_score, get_max_aminochain, skipper

# Importing random forest model

modelpath = os.path.dirname(os.path.abspath(__file__)) + '/RFC.dump'

Rf = load(open(modelpath, 'rb'))
# The function generate list of shuflled matrix
def make_shuffle_matrix(matrix, cpu, iterat):
    """
    The functuion generate massive of shuffled matrix.

    Parameters
    ----------
    matrix : pandas DataFrame
        PSSM profile.
    cpu : int
        Number of tred used.
    iterat : int
        Number of iterations of shuffling.
    Returns
    -------
    module_shuffling_matrix : list
        List of matrix, shuffled by module.
    substrate_shuffling_matrix : list
        List of matrix, shuffled by substrate.
    """
    module_shuffling_matrix = multi_thread_shuffling(matrix, ShufflingType='module', iterations=iterat, threads=cpu)
    substrate_shuffling_matrix = multi_thread_shuffling(matrix, ShufflingType='substrate', iterations=iterat, threads=cpu)
    return module_shuffling_matrix, substrate_shuffling_matrix

# The fujnction finds suquence with maximum possible value, results from alignment
def get_MaxSeq(matrix, variant_seq):
    """
    The functuion parallel calculation of scores for shuffled matrix.

    Parameters
    ----------
    matrix : pandas DataFrame
        PSSM profile.
    variant_seq : list
        Variant of core peptide chain.
    Returns
    -------
    shuffled_scores : list
        List of scores for shuffled matrix.
    """
    MaxSeq = []
    subs = matrix.keys()[1: ]
    # Find sequence, wich have maximum alignment score 
    for idx in matrix.index:

        MAX_value = max(list(matrix.iloc[idx][1:]))

        for key in subs:
            if matrix[key][idx] == MAX_value:

                MaxSeq.append(key) # If two smonomer have same value
                break
    # Making two variants of MaxSeq
    MaxSeq_full = MaxSeq.copy()
    MaxSeq_nan = MaxSeq.copy()
    
    for max_sub_idx in range(len(MaxSeq)):
        if variant_seq[max_sub_idx] == 'nan':

            MaxSeq_nan[max_sub_idx] = 'nan' # Adding nan to MaxSeq

    return MaxSeq_full, MaxSeq_nan
# The function gives an information about clusters
def get_cluster_info(table, BGC_ID, target_file):
    """
    The functuion return information about cluster.

    Parameters
    ----------
    table : pandas DataFrame
        Table with meta inforamtion about NRPS clusters.
    BGC_ID : str
        PSSM cluster ID.
    target_file : pandas DataFrame
        PSSM profile.
    Returns
    -------
    Name : str
        Cluster ID.
    Coord_cluster : str
        Coordinate of cluster.
    strand : str
        Strand of cluster.
    """
    for ind in table[table['ID'].str.contains(BGC_ID)].index:
        
        Name = table[table['ID'].str.contains(target_file.split('.')[0].split('_A_')[1])]['Name'][ind]
        Coord_cluster = table['Coordinates of cluster'][ind]
        strand = table['Gen strand'][ind]
        break

    return Name, Coord_cluster, strand

# Calculate scores 
def calculate_scores(variant_seq, matrix, substrate_shuffling_matrix, module_shuffling_matrix, cpu, iterat):    
    """
    Calculating scores.

    Parameters
    ----------
    variant_seq : list
        Variant of core peptide chain.
    matrix : pandas DataFrame
        PSSM profile.
    substrate_shuffling_matrix : list
        List of matrix, shuffled by substrate.
    module_shuffling_matrix : list
        List of matrix, shuffled by module.
    cpu : int
        Number of threads used.
    iterat : int
        Number of iterations of shuffling.
    Returns
    -------
    Sln_score : float

    Mln_score : float
    Slt_score : float
    Mlt_score : float
    Sdn_score : float
    Mdn_score : float
    Sdt_score : float
    Mdt_score : float
        Scores, which calculated with shuffling matrix by different variants.
        M - module shuffling                       S - substrate shuffling
        l - logarithmic transformation of score    d - raw score
        n - MaxSeq with nan replacement            t - MaxSeq without nan replacement
    Relative_score : float
        Relative score (Probability of target class)
    Binary : float
        Binary score of cluster matching.
    """
    # Finding suquence with maximum possible value, results from alignment
    MaxSeq_full, MaxSeq_nan = get_MaxSeq(matrix, variant_seq)
    # Calculating shuffled scores
    Sln_shuffled_score = array(multi_thread_calculating_scores(MaxSeq_nan, substrate_shuffling_matrix, type_value='log', iterations=iterat, threads=cpu))
    Mln_shuffled_score = array(multi_thread_calculating_scores(MaxSeq_nan, module_shuffling_matrix, type_value='log', iterations=iterat, threads=cpu))
    Slt_shuffled_score = array(multi_thread_calculating_scores(MaxSeq_full, substrate_shuffling_matrix, type_value='log', iterations=iterat, threads=cpu))
    Mlt_shuffled_score = array(multi_thread_calculating_scores(MaxSeq_full, module_shuffling_matrix, type_value='log', iterations=iterat, threads=cpu))
    Sdn_shuffled_score = array(multi_thread_calculating_scores(MaxSeq_nan, substrate_shuffling_matrix, type_value=None, iterations=iterat, threads=cpu))
    Mdn_shuffled_score = array(multi_thread_calculating_scores(MaxSeq_nan, module_shuffling_matrix, type_value=None, iterations=iterat, threads=cpu))
    Sdt_shuffled_score = array(multi_thread_calculating_scores(MaxSeq_full, substrate_shuffling_matrix, type_value=None, iterations=iterat, threads=cpu))
    Mdt_shuffled_score = array(multi_thread_calculating_scores(MaxSeq_full, module_shuffling_matrix, type_value=None, iterations=iterat, threads=cpu))
    # Calculating scores for target sequence
    log_target_score = get_score(variant_seq, matrix, type_value='log')
    non_log_target_score = get_score(variant_seq, matrix, type_value=None)
    # Calculating features scores
    Sln_score = len(Sln_shuffled_score[Sln_shuffled_score < log_target_score])/len(Sln_shuffled_score)
    Mln_score = len(Mln_shuffled_score[Mln_shuffled_score < log_target_score])/len(Mln_shuffled_score)
    Slt_score = len(Slt_shuffled_score[Slt_shuffled_score < log_target_score])/len(Slt_shuffled_score)
    Mlt_score = len(Mlt_shuffled_score[Mlt_shuffled_score < log_target_score])/len(Mlt_shuffled_score)
    Sdn_score = len(Sdn_shuffled_score[Sdn_shuffled_score < non_log_target_score])/len(Sdn_shuffled_score)
    Mdn_score = len(Mdn_shuffled_score[Mdn_shuffled_score < non_log_target_score])/len(Mdn_shuffled_score)
    Sdt_score = len(Sdt_shuffled_score[Sdt_shuffled_score < non_log_target_score])/len(Sdt_shuffled_score)
    Mdt_score = len(Mdt_shuffled_score[Mdt_shuffled_score < non_log_target_score])/len(Mdt_shuffled_score)
    # Calculating Relative score
    Relative_score = round(Rf.predict_proba([[Sln_score, Mln_score, 
                                        Sdn_score, Mdn_score,
                                        Sdt_score, Mdt_score,
                                        Slt_score, Mlt_score  
                                        ]])[0][1], 3)
    Binary = Rf.predict([[Sln_score, Mln_score, 
                                        Sdn_score, Mdn_score,
                                        Sdt_score, Mdt_score,
                                        Slt_score, Mlt_score  
                                        ]])[0]
    return Sln_score, Mln_score, Slt_score, Mlt_score, Sdn_score, Mdn_score, Sdt_score, Mdt_score, Relative_score, Binary

def give_results(tsv_out, folder, files, table, ID, PeptideSeq, skip, cpu, iterat):
    """
    The functuion return information about cluster.

    Parameters
    ----------
    tsv_out : dict
        Empty dictionary for adding results.
    folder : str
        Path to PSSMs.
    files : list
        List of PSSMs.
    table : pandas DataFrame
        Table with meta inforamtion about NRPS clusters.
    ID : str
        Name of substance.
    PeptideSeq : dict
        Core peptide chains for different biosynthesis types (e.g. A, B, or C).
    kip : int
        Number of presumptive skip.
    cpu : int
        Number of threads used.
    iterat : int
        Number of iterations of shuffling.
    Returns
    -------
    tsv_out : dict
        Full dictionary for adding results.
    """
    for target_file in files:
            
        try:

            BGC_ID = target_file.split('.')[0].split('_A_')[1]

        except:

            continue

        if '_A_' not in target_file:
            continue

        Name, Coord_cluster, strand = get_cluster_info(table, BGC_ID, target_file) # Getting information about cluster
        BGC = read_csv(folder + target_file, sep='\t')
        # Skipping mode
        if skip == 0:
                
            BGC = [BGC]
                
        else:
                
            BGC == skipper(BGC, skip)

        for matrix in BGC:
            # Check quality of matrix
            if len(matrix) == 1:
                continue
            
            check = 0
            values = matrix.drop(matrix.columns[0], axis=1).values

            for i in values:
                if all(i) == 0:

                    check += 1

            if check == len(values): # If thes condition is True, the matrix of unrecognized monomers 
                continue

            # Generating shuffling matrix
            module_shuffling_matrix, substrate_shuffling_matrix =  make_shuffle_matrix(matrix, cpu, iterat)

            for BS_type in PeptideSeq:# For every biosynthesis profile pathways

                if PeptideSeq[BS_type] == None: # If in sequence only nan monomers
                    continue

                if len(PeptideSeq[BS_type]) == 0: # If have not the variant
                    continue

                # Check correctness of PeptideSeq
                length_max= get_max_aminochain(PeptideSeq[BS_type])
                EPs = make_combine(PeptideSeq[BS_type], length_max, matrix, delta=3)
                
                if EPs is None: # If length sequnce can't be scaled to cluster size
                    continue

                for variant_seq in EPs:
                    
                    Sln_score, Mln_score, Slt_score, Mlt_score, Sdn_score, Mdn_score, Sdt_score, Mdt_score, Relative_score, Binary = calculate_scores(variant_seq, matrix, substrate_shuffling_matrix, module_shuffling_matrix, cpu, iterat)
                    #Recordind dictionary 
                    tsv_out['Chromosome ID'].append(Name)
                    tsv_out['Coordinates of cluster'].append(Coord_cluster)
                    tsv_out['Strand'].append(strand)
                    tsv_out['Substance'].append(ID)
                    tsv_out['BGC ID'].append(BGC_ID)
                    tsv_out['Putative linearized NRP sequence'].append('--'.join(variant_seq))
                    tsv_out['Biosynthesis profile'].append('Type {}'.format(BS_type))
                    tsv_out['Sln score'].append(Sln_score) #shaffling substrates in matrix with log score and nan in maximally possible sequence
                    tsv_out['Mln score'].append(Mln_score) #shaffling modules matrix with log score and nan in maximally possible sequence
                    tsv_out['Sdn score'].append(Sdn_score) #shaffling substrates matrix without log score and nan in maximally possible sequence
                    tsv_out['Mdn score'].append(Mdn_score) #shaffling modules matrix without log score and nan in maximally possible sequence
                    tsv_out['Sdt score'].append(Sdt_score) #shaffling substrates matrix without log score in maximally possible sequence
                    tsv_out['Mdt score'].append(Mdt_score) #shaffling modules matrix without log score in maximally possible sequence
                    tsv_out['Slt score'].append(Slt_score) #shaffling substrates matrix with log score in maximally possible sequence
                    tsv_out['Mlt score'].append(Mlt_score) #shaffling modules matrix with log score in maximally possible sequence
                    tsv_out['Relative score'].append(Relative_score) #Final score
                    tsv_out['Binary'].append(Binary) #Binary value
                    
    return tsv_out

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