def DP(mole, ref):
MIN_SCORE = -10000
cols = len(ref)
rows = len(mole)
score_matrix = [[MIN_SCORE for col in range(cols + 1)] for row in range(rows + 1)]
for i in xrange(len(score_matrix[0])):
score_matrix[0][i] = 0
map_matrix = [[(-1, -1) for col in range(cols + 1)] for row in range(rows + 1)]
for i in xrange(rows):
i += 1
for j in xrange(cols):
j += 1
score_matrix[i][j] = score_matrix[i - 1][j - 1] + score.valid_score(mole[i - 1 : i], ref[j - 1 : j])
map_matrix[i][j] = (i - 1, j - 1)
#DELETE: 3 is the max number of delete
k = 0
if j - 5 > 0:
k = j - 5
while k < j - 1:
s = score_matrix[i - 1][k] + score.valid_score(mole[i - 1 : i], ref[k : j])
if s > score_matrix[i][j]:
score_matrix[i][j] = s
map_matrix[i][j] = (i - 1, k)
k += 1
#INSERT: 3 is the max number of insert
k = 0
if i - 5 > 0:
k = i - 5
while k < i - 1:
s = score_matrix[k][j - 1] + score.valid_score(mole[k : i], ref[j - 1 : j])
if s > score_matrix[i][j]:
score_matrix[i][j] = s
map_matrix[i][j] = (k, j - 1)
k += 1
if i > 3 and j > 3:
s = score_matrix[i - 2][j - 2] + score.valid_score(mole[i - 2 : i], ref[j - 2 : j])
if s > score_matrix[i][j]:
score_matrix[i][j] = s
map_matrix[i][j] = (i - 2, j - 2)
#the result is in the last row
last_row = score_matrix[rows]
best_score = last_row[1]
end_site = 1
#get the best score of last row
for j in xrange(cols):
j += 1
if best_score < last_row[j]:
best_score = last_row[j]
end_site = j
(pre_row, pre_col) = map_matrix[rows][end_site]
while pre_row > 1:
(pre_row, pre_col) = map_matrix[pre_row][pre_col]
#print '%f '%last_row[end_site],
print '%d '%pre_col,
print '%d '%end_site
'''
def DP(mole, ref):
MIN_SCORE = -10000
cols = len(ref)
rows = len(mole)
score_matrix = [[MIN_SCORE for col in range(cols + 1)] for row in range(rows + 1)]
for i in xrange(len(score_matrix[0])):
score_matrix[0][i] = 0
map_matrix = [[-1 for col in range(cols + 1)] for row in range(rows + 1)]
for i in xrange(rows):
i += 1
for j in xrange(cols):
j += 1
score_matrix[i][j] = score_matrix[i - 1][j - 1] + score.valid_score(mole[i - 1 : i], ref[j - 1 : j])
map_matrix[i][j] = (i - 1) * cols + (j - 1)
#DELETE: 3 is the max number of delete
k = 0
if j - 5 > 0:
k = j - 5
while k < j - 1:
s = score_matrix[i - 1][k] + score.valid_score(mole[i - 1 : i], ref[k : j])
if s > score_matrix[i][j]:
score_matrix[i][j] = s
map_matrix[i][j] = (i - 1) * cols + k
k += 1
#INSERT: 3 is the max number of insert
k = 0
if i - 5 > 0:
k = i - 5
while k < i - 1:
s = score_matrix[k][j - 1] + score.valid_score(mole[k : i], ref[j - 1 : j])
if s > score_matrix[i][j]:
score_matrix[i][j] = s
map_matrix[i][j] = k * cols + (j - 1)
k += 1
#the result is in the last row
last_row = score_matrix[rows]
best_score = last_row[1]
end_site = 1
#get the best score of last row
for j in xrange(cols):
j += 1
if best_score < last_row[j]:
best_score = last_row[j]
end_site = j
print '#####################'
print end_site
print '#####################'
'''
