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#cython: language_level=3
cdef import from "stdlib.h":
void* malloc(int size) except NULL
void* realloc(void* chunk,int size) except NULL
void free(void* chunk)
cdef import from "string.h":
void bzero(void *s, size_t n)
void memset(void* chunk,int car,int length)
void memcpy(void* s1, void* s2, int n)
cdef struct AlignCell :
double score
int path
cdef struct AlignMatrix :
AlignCell* matrix
int* bestVJump
int* bestHJump
int msize
int vsize
int hsize
cdef AlignMatrix* allocateMatrix(int hsize, int vsize,AlignMatrix *matrix=?)
cdef void freeMatrix(AlignMatrix* matrix)
cdef void resetMatrix(AlignMatrix* matrix)
cdef struct alignSequence:
long length
long buffsize
bint hasQuality
char* sequence
double* quality
cdef alignSequence* allocateSequence(object bioseq, alignSequence* seq=?) except *
cdef void freeSequence(alignSequence* seq)
cdef struct alignPath:
long length
long buffsize
long vStart
long hStart
long *path
cdef alignPath* allocatePath(long l1,long l2,alignPath* path=?)
cdef void reversePath(alignPath* path)
cdef void freePath(alignPath* path)
cdef int bitCount(int x)
cpdef bint iupacMatch(unsigned char a, unsigned char b)
cpdef double iupacPartialMatch(unsigned char a, unsigned char b)
cpdef unsigned char encodeBase(unsigned char lettre)
cdef class DynamicProgramming:
cdef AlignMatrix* matrix
cdef object horizontalSeq
cdef object verticalSeq
cdef alignSequence* hSeq
cdef alignSequence* vSeq
cdef alignPath* path
cdef double _opengap
cdef double _extgap
cdef object alignment
cdef bint sequenceChanged
cdef bint scoreChanged
cdef int _vlen(self)
cdef int _hlen(self)
cdef int allocate(self) except -1
cdef double doAlignment(self) except? 0
cdef void reset(self)
cdef inline int index(self, int x, int y)
cdef inline bint _needToCompute(self)
cdef void backtrack(self)
cdef void clean(self)
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