void mixMarkov(vector< vector<int> >& X, int trainingNum, int numOfState,
int K, vector<double>& pi, vector< vector<double> >& thetaInit,
vector< vector< vector<double> > >& thetaTrans) {
vector < vector< map<int, int> > > sigma;
vector<double> ll_variables(3);
vector< vector<double> > condProb(trainingNum);
initVariable(pi, thetaInit, thetaTrans);
setSigma(X, sigma, trainingNum);
estep(X, pi, thetaInit, thetaTrans, condProb);
ll_variables = computeLL(X, thetaInit, thetaTrans);
for (iter = 1; iter<= MAX_ITER; ++iter) {
mstep(pi, thetaInit, thetaTrans, condProb);
estep(X, pi, thetaInit, thetaTrans, condProb);
vector<double> new_ll_variables(3);
new_ll_variables = computeLL(X, thetaInit, thetaTrans);
//check for convergence
if (new_ll_variables[0] + new_ll_variables[1] + new_ll_variables[2] - (ll_variables[0] + ll_variables[1] + ll_variables[2]) >TOL ) {
ll_variables = new_ll_variables;
} else {
break;
}
}
}
/*
* An implementation of Boyer-Moore algorithm with bad character rule and good suffix rule.
*/
int fastfastBMmatcher(int n, int m){
int R[28];
/*
* Zbar[i] is the lenght of the longest suffix of P[1,2,...,i]
* matched with a suffix of P[1,2,..,m]
*/
int Zbar[MAXM];
/*
* LL[i] is the maximum index smaller than m such that P[i,i+1,..,m]
* matched with a suffix of P[1,2,..,LL[i]] such that the char to the left of
* of the matched substring of P[1,2,..,LL[i]] is not equal from P[i-1]
*/
int LL[MAXM];
/*
* SL[i] is the length of the longest suffix of P[i,i+1,..,m] that is matched with
* a prefix of P[1,2,...,m]
*/
int SL[MAXM];
badCharBackup(m,R);
int i = 1, j = 0, p = 0, skip = 0;
memset(Zbar, 0, sizeof(Zbar)); // set everything to 0
memset(LL,0,sizeof(LL));// set everything to 0
memset(SL,0, sizeof(SL));// set everything to 0
computeLL(m, LL, Zbar);
computeSL(m, SL, Zbar);
while(i <= n-m+1){
skip = 0;
j = m;
while(j >= 1 && skip == 0){
if(T[i+j-1] != P[j]){
p = T[i+j-1]-96;
skip = max(1, j - R[p]); // skip by the bad character rule;
if(j!=m){
if(LL[j+1] !=0){
skip = max(skip, m - LL[j+1]);// (1) and (2) of the good suffix rule
} else {
skip = max(skip, m - SL[j+1]);// (3) and (4) of the good suffix rule
/*
* For more information about the rules, see .... blogpost
*/
}
}
}
j--;
}
if(skip == 0) return i;
i = i + skip;
}
return -1;
}
JNIEXPORT jlong JNICALL Java_edu_biu_scapi_primitives_dlog_miracl_MiraclDlogECFp_simultaneousMultiplyFp
(JNIEnv *env, jobject obj, jlong m, jlongArray elements, jobjectArray exponents){
int size = env->GetArrayLength(elements); //number of points
jlong* longElements = env->GetLongArrayElements(elements, 0); //convert JllongArray to long array
epoint ** points = (epoint**) calloc(size, sizeof(epoint*)); //create a big array to hold the points
big* bigExponents = (big*) calloc(size, sizeof(big)); //create a big array to hold the exponents
int i;
epoint *p;
jbyteArray exponent;
/* convert the accepted parameters to MIRACL parameters*/
miracl* mip = (miracl*)m;
for(i=0; i<size; i++){
points[i] = (epoint*) longElements[i];
exponent = (jbyteArray) env->GetObjectArrayElement(exponents, i);
bigExponents[i] = byteArrayToMiraclBig(env, mip, exponent);
}
// p = epoint_init(mip);
//ecurve_multn(mip, size, bigExponents, points, p);
p = computeLL(mip, points, bigExponents, size, 1);
//release the memory
for(i=0; i<size; i++){
mirkill(bigExponents[i]);
}
free(points);
free(bigExponents);
//release jbyte
env ->ReleaseLongArrayElements(elements, longElements, 0);
return (jlong)p; //return the result
}
