//计算DNA k-mer的哈希索引，但是这个索引的长度为0 - 3*sigma(4^(k-1))(k=1...k)
//当kmer的长度为3时，索引的范围是0-63
int indexOfKmer(char* kmer)
{
int idx = 0;
int i;
int l = strlen(kmer);
int *N;
//calloc会把内存初始化为0
N = (int*)calloc(256, sizeof(int));
//使用ascii码作为索引
N['A'] = 0;
N['C'] = 1;
N['T'] = 2;
N['G'] = 3;
for (i=0; i<l; i++) {
idx += N[ (int)(kmer[i]) ] * powint(4,(l - i - 1));
}
free(N);
return idx;
}
VOID InitRayTreeStack(INT TreeDepth, INT pid)
{
raystruct[pid].StackSize = powint(2, TreeDepth) - 1;
raystruct[pid].StackSize += NumSubRays;
raystruct[pid].Stack = (RAY *)LocalMalloc(raystruct[pid].StackSize*sizeof(RAY), "raystack.c");
raystruct[pid].StackTop = -1; /* Empty condition. */
}
RCP<const Number> Integer::pow_negint(const Integer &other) const {
RCP<const Number> tmp = powint(*other.neg());
if (is_a<Integer>(*tmp)) {
mpq_class q(sgn(rcp_static_cast<const Integer>(tmp)->i), abs(rcp_static_cast<const Integer>(tmp)->i));
return make_rcp<const Rational>(q);
} else {
throw std::runtime_error("powint returned non-integer");
}
}
RCP<const Number> Integer::pow_negint(const Integer &other) const
{
RCP<const Number> tmp = powint(*other.neg());
if (is_a<Integer>(*tmp)) {
const integer_class &j = down_cast<const Integer &>(*tmp).i;
#if SYMENGINE_INTEGER_CLASS == SYMENGINE_BOOSTMP
// boost::multiprecision::cpp_rational lacks an (int, cpp_int)
// constructor. must use cpp_rational(cpp_int,cpp_int)
rational_class q(integer_class(mp_sign(j)), mp_abs(j));
#else
rational_class q(mp_sign(j), mp_abs(j));
#endif
return Rational::from_mpq(std::move(q));
} else {
throw SymEngineException("powint returned non-integer");
}
}
// doubledouble^int
doubledouble powint(const doubledouble& u, const int c) {
if (c<0) return recip(powint(u,-c));
switch (c) {
case 0: return u.h()==0.0?doubledouble(pow(0.0,0.0)):doubledouble(1.0); // let math.h handle 0^0.
case 1: return u;
case 2: return sqr(u);
case 3: return sqr(u)*u;
default: { // binary method
int n=c, m; doubledouble y=1.0, z=u; if (n<0) n=-n;
while (1) {
m=n; n/=2;
if (n+n!=m) { // if m odd
y*=z; if (0==n) return y;
}
z=sqr(z);
}
}
}
}
