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#cython: language_level=3
'''
Created on 6 Nov. 2009
@author: coissac
'''
cdef class FreeEndGap(NWS):
def __init__(self,match=4,mismatch=-6,opengap=-8,extgap=-2):
NWS.__init__(self,match,mismatch,opengap,extgap)
self.xsmax=0
self.xmax=0
cdef double doAlignment(self) except? 0:
cdef int i # vertical index
cdef int j # horizontal index
cdef int idx
cdef int idx0
cdef int idx1
cdef int jump
cdef int delta
cdef double score
cdef double scoremax
cdef int path
assert self.hSeq.length > self.vSeq.length, \
"Sequence B must be shorter than sequence A"
if self.needToCompute:
self.allocate()
self.reset()
self.xsmax=0
self.xmax=0
for j in range(1,self.hSeq.length+1):
idx = self.index(j,0)
self.matrix.matrix[idx].score = 0
self.matrix.matrix[idx].path = j
for i in range(1,self.vSeq.length+1):
idx = self.index(0,i)
self.matrix.matrix[idx].score = self._opengap + (self._extgap * (i-1))
self.matrix.matrix[idx].path = -i
idx0=self.index(-1,0)
idx1=self.index(0,1)
for i in range(1,self.vSeq.length+1):
idx0+=1
idx1+=1
for j in range(1,self.hSeq.length+1):
# 1 - came from diagonal
#idx = self.index(j-1,i-1)
idx = idx0
# print "computing cell : %d,%d --> %d/%d" % (j,i,self.index(j,i),self.matrix.msize),
scoremax = self.matrix.matrix[idx].score + \
self.matchScore(j,i)
path = 0
# print "so=%f sd=%f sm=%f" % (self.matrix.matrix[idx].score,self.matchScore(j,i),scoremax),
# 2 - open horizontal gap
# idx = self.index(j-1,i)
idx = idx1 - 1
score = self.matrix.matrix[idx].score+ \
self._opengap
if score > scoremax :
scoremax = score
path = +1
# 3 - open vertical gap
# idx = self.index(j,i-1)
idx = idx0 + 1
score = self.matrix.matrix[idx].score + \
self._opengap
if score > scoremax :
scoremax = score
path = -1
# 4 - extend horizontal gap
jump = self.matrix.bestHJump[i]
if jump >= 0:
idx = self.index(jump,i)
delta = j-jump
score = self.matrix.matrix[idx].score + \
self._extgap * delta
if score > scoremax :
scoremax = score
path = delta+1
# 5 - extend vertical gap
jump = self.matrix.bestVJump[j]
if jump >= 0:
idx = self.index(j,jump)
delta = i-jump
score = self.matrix.matrix[idx].score + \
self._extgap * delta
if score > scoremax :
scoremax = score
path = -delta-1
# idx = self.index(j,i)
idx = idx1
self.matrix.matrix[idx].score = scoremax
self.matrix.matrix[idx].path = path
if path == -1:
self.matrix.bestVJump[j]=i
elif path == +1 :
self.matrix.bestHJump[i]=j
if i==self.vSeq.length and scoremax > self.xsmax:
self.xsmax=scoremax
self.xmax=j
idx0+=1
idx1+=1
self.sequenceChanged=False
self.scoreChanged=False
return self.xsmax
cdef void backtrack(self):
#cdef list path=[]
cdef int i
cdef int j
cdef int p
self.doAlignment()
j=self.xmax
i=self.vSeq.length
self.path=allocatePath(i,j+1,self.path)
if self.xmax<self.hSeq.length:
self.path.path[self.path.length]=self.hSeq.length-self.xmax
self.path.length+=1
while (i or j):
p=self.matrix.matrix[self.index(j,i)].path
self.path.path[self.path.length]=p
self.path.length+=1
#path.append(p)
if p==0:
i-=1
j-=1
elif p < 0:
i+=p
else:
j-=p
#path.reverse()
#reversePath(self.path)
self.path.hStart=0
self.path.vStart=0
#return 0,0,path
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