import scoringMatrix


seq1 = open("seq1.txt",'r').read() # read the two sequences
seq2 = open("seq2.txt",'r').read()
print(seq1)  # print them just to make sure they were read properly
print(seq2) 

# create the matrix of scores and of directions
scorematrix = [[0] * (len(seq1)+1) for _ in range(len(seq2)+1)]
directionmatrix = [[8] * (len(seq1)+1) for _ in range(len(seq2)+1)]

# Fill in the first column, the first row is done below
for i in range(0,len(seq2)+1):
    scorematrix[i][0] = 0 # -8*i
    directionmatrix[i][0] = 'v'

threshold = 20  # set the cut-off threshold

for i in range(1,len(seq1)+1): # column 
    for j in range(0,len(seq2)+1): # row, start at 0
        v = scorematrix[j-1][i] + scoringMatrix.gappenalty
        h = scorematrix[j][i-1] + scoringMatrix.gappenalty
        x = scoringMatrix.aminoDictionary[seq1[i-1]]
        y = scoringMatrix.aminoDictionary[seq2[j-1]]
        d = scorematrix[j-1][i-1] + scoringMatrix.blosum50[x][y]
        if(j == 0): # if in row 0 use the "special" rule for values
            best = scorematrix[0][i-1] # best score so far
            besty = 0
            for y in range(1,len(seq2)+1): # check each value in the previous column
                if(scorematrix[y][i-1]-threshold > best): # if the score is better than the best so far
                    best = scorematrix[y][i-1]-threshold  # remember the score
                    besty = y                             # remember the row the score came from
            scorematrix[0][i] = best # store the best score found
            if(besty == 0):
                directionmatrix[0][i] = 'h' # horizontal move
            else:
                directionmatrix[0][i] = besty # jump down in the previous column
            
        else:  # if not in the first row, use the "normal" method to caluculate the score
            scorematrix[j][i] = max(scorematrix[0][i],v,h,d)
            if(v == max(scorematrix[0][i],v,h,d)):
                directionmatrix[j][i] = 'v' # vertical move
            if(h == max(scorematrix[0][i],v,h,d)):
                directionmatrix[j][i] = 'h' # horizontal move
            if(d == max(scorematrix[0][i],v,h,d)):
                directionmatrix[j][i] = 'd' # diagonal move
            if(scorematrix[0][i] == max(scorematrix[0][i],v,h,d)):
                directionmatrix[j][i] = 'r' # jump to the top row

for j in range(0,len(seq2)+1):
    for i in range(0,len(seq1)+1):
        print(scorematrix[j][i], end =" ")
    print()


print()
print()

for j in range(0,len(seq2)+1):
    for i in range(0,len(seq1)+1):
        print(directionmatrix[j][i], end =" ")
    print()

x = len(seq1) # start at the top right corner (technically one to the right of that)
y = 0
print("Score = ",scorematrix[y][x])
alignedseq1 = []
alignedseq2 = []
while(x != 0):  # while not at the left edge of the table
    if(directionmatrix[y][x] == 'd'): # diagonal
        x = x - 1   # x -= 1 or x--
        y = y - 1
        alignedseq1.append(seq1[x])
        alignedseq2.append(seq2[y])
        #print("seq1[x], " ", seq2[y]);
    elif(directionmatrix[y][x] == 'v'): # vertical
        y = y - 1
        alignedseq1.append('_')
        alignedseq2.append(seq2[y])
        #print("_", " ", seq2[y])
    elif(directionmatrix[y][x] == 'h'): # horizontal
        x = x - 1
        alignedseq1.append(seq1[x])
        alignedseq2.append('_')
        #print(seq1[x], " ", "_")
    elif(directionmatrix[y][x] == 'r'): # toprow
        y = 0 # jump to top row
        #alignedseq1.append(seq2[y])
        #alignedseq2.append('.')
        #print(seq1[x], " ", "_")
    else:  # jump down in previous column
        y = directionmatrix[y][x]
        x = x - 1
        alignedseq1.append(seq1[x])
        alignedseq2.append(".")
        #print(seq1[x], " ", "_")

#print(alignedseq1) # just extra output
#print(alignedseq2)
alignedseq1.reverse()
alignedseq2.reverse()
print(''.join(alignedseq1))
print(''.join(alignedseq2))