String-kernel/gapkernel.cpp at master · arnomoonens/String-kernel · GitHub

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#include<Rcpp.h>
#include<math.h>// pow
usingnamespaceRcpp;

// [[Rcpp::export]]
longdoublecppKernel(std::string x, std::string y, double lambda, unsignedint p) {
int r = x.length();
int c = y.length();
unsignedint i = 0, j = 0;
longdouble **A = newlongdouble* [r];
longdouble **B = newlongdouble* [r+1];

 B[0] = newlongdouble[c+1];
for(i = 0; i < r; i++) {
 A[i] = newlongdouble[c];
 B[i+1] = newlongdouble[c+1];
for(j = 0; j < c; j++) {
 B[i][j] = 0;
 B[i+1][j+1] = 0;
 A[i][j] = (x[i] == y[j] ? pow(lambda, 2) : 0);
 }
 }
longdouble* k = newlongdouble[p];
 k[0] = 0;
for(int l = 1; l < p; l++) {
 k[l] = 0;
for(i = 0; i < r; i++) {
for(j = 0; j < c; j++) {
 B[i+1][j+1] = A[i][j] + lambda * B[i][j+1] + lambda * B[i+1][j] - pow(lambda, 2) * B[i][j];
if(x[i] == y[j]) {
 A[i][j] = pow(lambda, 2) * B[i][j];
 k[l] = k[l] + A[i][j];
 }
 }
 }
 }
delete[] B[0];
for(i = 0; i < r; i++) {
delete[] A[i];
delete[] B[i+1];
 }
delete[] A;
delete[] B;
longdouble result = k[p-1];
delete[] k;
return result;
}


// (test) code to run after compilation
/*** R

*/