157 lines
5.3 KiB
Cython
Executable File
157 lines
5.3 KiB
Cython
Executable File
#cython: language_level=3
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'''
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Created on 6 Nov. 2009
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@author: coissac
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'''
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cdef class RightDirectAssemble(NWS):
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def __init__(self,match=4,mismatch=-6,opengap=-8,extgap=-2):
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NWS.__init__(self,match,mismatch,opengap,extgap)
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self.xsmax=0
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self.xmax=0
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cdef double doAlignment(self) except? 0:
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cdef int i # vertical index
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cdef int j # horizontal index
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cdef int idx
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cdef int jump
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cdef int delta
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cdef double score
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cdef double scoremax
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cdef int path
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if self.needToCompute:
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self.allocate()
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self.reset()
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self.xsmax=0
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self.xmax=0
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for j in range(1,self.hSeq.length+1):
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idx = self.index(j,0)
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self.matrix.matrix[idx].score = self._opengap + (self._extgap * (j-1))
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self.matrix.matrix[idx].path = j
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for i in range(1,self.vSeq.length+1):
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idx = self.index(0,i)
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self.matrix.matrix[idx].score = 0
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self.matrix.matrix[idx].path = -i
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for i in range(1,self.vSeq.length+1):
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for j in range(1,self.hSeq.length+1):
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# 1 - came from diagonal
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idx = self.index(j-1,i-1)
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#print("computing cell : %d,%d --> %d/%d" % (j,i,self.index(j,i),self.matrix.msize),)
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scoremax = self.matrix.matrix[idx].score + \
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self.matchScore(j,i)
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path = 0
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#print("so=%f sd=%f sm=%f" % (self.matrix.matrix[idx].score,self.matchScore(j,i),scoremax),)
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# 2 - open horizontal gap
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idx = self.index(j-1,i)
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score = self.matrix.matrix[idx].score+ \
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self._opengap
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if score > scoremax :
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scoremax = score
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path = +1
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# 3 - open vertical gap
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idx = self.index(j,i-1)
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score = self.matrix.matrix[idx].score + \
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self._opengap
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if score > scoremax :
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scoremax = score
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path = -1
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# 4 - extend horizontal gap
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jump = self.matrix.bestHJump[i]
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if jump >= 0:
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idx = self.index(jump,i)
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delta = j-jump
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score = self.matrix.matrix[idx].score + \
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self._extgap * delta
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if score > scoremax :
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scoremax = score
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path = delta+1
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# 5 - extend vertical gap
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jump = self.matrix.bestVJump[j]
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if jump >= 0:
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idx = self.index(j,jump)
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delta = i-jump
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score = self.matrix.matrix[idx].score + \
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self._extgap * delta
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if score > scoremax :
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scoremax = score
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path = -delta-1
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idx = self.index(j,i)
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self.matrix.matrix[idx].score = scoremax
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self.matrix.matrix[idx].path = path
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if path == -1:
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self.matrix.bestVJump[j]=i
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elif path == +1 :
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self.matrix.bestHJump[i]=j
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if i==self.vSeq.length and scoremax > self.xsmax:
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self.xsmax=scoremax
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self.xmax=j
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self.sequenceChanged=False
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self.scoreChanged=False
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return self.xsmax
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cdef void backtrack(self):
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cdef list path=[]
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cdef int i
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cdef int j
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cdef int p
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self.doAlignment()
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j=self.xmax
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i=self.vSeq.length
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self.path=allocatePath(i,j+1,self.path)
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if self.xmax<self.hSeq.length:
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self.path.path[self.path.length]=self.hSeq.length-self.xmax
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self.path.length+=1
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while (i or j):
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p=self.matrix.matrix[self.index(j,i)].path
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self.path.path[self.path.length]=p
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self.path.length+=1
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#path.append(p)
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if p==0:
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i-=1
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j-=1
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elif p < 0:
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i+=p
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else:
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j-=p
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#path.reverse()
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self.path.hStart=0
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self.path.vStart=0
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#reversePath(self.path)
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#return 0,0,path
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cdef class RightReverseAssemble(RightDirectAssemble):
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property seqB:
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def __get__(self):
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return self.verticalSeq.wrapped
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def __set__(self, seq):
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self.sequenceChanged=True
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self.verticalSeq=seq.reverse_complement
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self.vSeq=allocateSequence(self.verticalSeq,self.vSeq)
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