void RcompoundpoissonPape_useGamma(double *gamma,
double *hitdistribution, int *nseq, int *lseq, int * mhit, int *mclump) {
int seqlen, i;
int maxclumpsize, maxhits;
double lambda;
double *theta, extention[3];
if (!Rpwm||!Rcpwm||!Rstation||!Rtrans) {
error("load forground and background properly");
return;
}
if (!gamma||!hitdistribution||!nseq||!lseq||!mhit||!mclump) {
error("parameters are null");
return;
}
if (Rgran==0.0 || Rsiglevel==0.0) {
error("call mdist.option first");
return;
}
seqlen=0;
for (i=0; i<*nseq; i++) {
seqlen+=lseq[i]-Rpwm->nrow+1;
}
maxclumpsize=(double)mclump[0];
maxhits=(double)mhit[0];
memset(extention, 0, 3*sizeof(double));
gamma[Rpwm->nrow]=(gamma[Rpwm->nrow]+EPSILON)/(1+2*EPSILON);
computeExtentionFactorsPape(extention, gamma, Rpwm->nrow);
theta=initTheta(maxclumpsize);
if (theta==NULL) {
error("Memory-allocation in initTheta failed");
}
computeInitialClump(theta, gamma,Rpwm->nrow);
computeTheta(maxclumpsize, theta, extention, Rpwm->nrow);
lambda=computePoissonParameter(seqlen, Rpwm->nrow,
maxclumpsize, gamma[0],theta);
computeCompoundPoissonDistributionKemp(lambda, maxhits,
maxclumpsize, theta, hitdistribution);
deleteTheta(theta);
}
const SUCCESS PhysicalObject::collided(PhysicalObject &object, const Radians angle)
{
Vector initVec(getVelocity()-object.getVelocity());
Mag_t<double> initVel(initVec.mag());
Radians initTheta(initVec.theta());
if(fabs(getX(initVel, initTheta-angle)) < REST_THRESHOLD)
{
setVelocity(getVelocity()+initVec/2.0);
object.setVelocity(object.getVelocity()-initVec/2.0);
antigravitate(object);
object.antigravitate(*this);
return SUCCEEDED;
}
// Frame of reference with the object at rest with this approaching it with an angle of 0
Point<double> p2(Vector(Mag_t<double>(2.0*getMass()*getX(initVel, initTheta-angle)/(getMass()+object.getMass())), initTheta-angle)); // Gets the velocity of 2 based on elastic collision equation
Point<double> p1((initVel*getMass()-p2.x()*object.getMass())/getMass(), -p2.y()*object.getMass()/getMass()); // Gets the velocity of 1 based off of elastic collision rulez
if(fabs(p1.x()) < REST_THRESHOLD && fabs(p2.x()) < REST_THRESHOLD)
{
p1.x(0.0);
p2.x(0.0);
}
Vector v1(p1);
Vector v2(p2);
v1.theta(-v1.theta()+initTheta);
v2.theta(angle);
v1 += object.getVelocity();
v2 += object.getVelocity();
Point<double> dif(object.getPosition()-*position);
while(getCollider()->collides(*object.getCollider()))
acceleration.set(*position-dif/pythagoras<double>(dif));
setVelocity(v1);
object.setVelocity(v2);
return SUCCEEDED;
}
void initTrain() {
initTheta();
mybeta = (double **) malloc(sizeof(double*)*M);
for (int m = 0; m < M; m++) {
mybeta[m] = (double*) malloc(sizeof(double)*K);
for (int k = 0; k < K; k++) {
mybeta[m][k] = 1;
}
}
myalpha = (double *) malloc(sizeof(double)*K);
for (int k = 0; k < K; k++) {
myalpha[k] = 1.0/M;
}
r = (double ***) malloc(sizeof(double**)*M);
for (int m = 0; m < M; m++) {
r[m] = (double**) malloc(sizeof(double*)*N[m]);
for (int n = 0; n < N[m]; n++) {
r[m][n] = (double*) malloc(sizeof(double)*K);
for (int k = 0; k < K; k++) {
r[m][n][k] = 0;
}
}
}
#ifdef NEW_PRIOR
int total = 0;
for (int m = 0; m < M; m++) {
total += N[m];
}
A = (double *) malloc(sizeof(double)*L);
B = (double *) malloc(sizeof(double)*L);
for (int l = 0; l < L; l++ ){
A[l] = 1;
B[l] = 1;
}
A[56] = B[56] = 0; //Internet do not use this
B[1] = B[2] = B[21] = B[67] = B[26] = B[69] = B[113] = B[76] = B[87] = B[54] = 2*total; // high prior for this
B[68] = B[71] = B[74] = B[81] = B[82] = B[84] = B[83] = B[73] = B[64] = B[112] = B[116] = B[120] = B[116] = B[120] = B[116] = B[114] = B[65] = B[47] = B[19] = B[20] = total; // low prior for this
#endif
}
void Rcompoundpoisson_useBeta(double *alpha, double *beta,
double *beta3p, double *beta5p,
double *hitdistribution, int *nseq,
int *lseq, int * mhit, int *mclump, int *sstrand) {
int seqlen, i;
int maxclumpsize, maxhits, singlestranded;
double lambda;
double *theta, extention[3];
double *delta, *deltap;
if (!Rpwm||!Rcpwm||!Rstation||!Rtrans) {
error("load forground and background properly");
return;
}
if (!alpha||!beta||!beta3p||!beta5p||
!hitdistribution||!nseq||!lseq||!mhit||!mclump) {
error("parameters are null");
return;
}
if (Rgran==0.0 || Rsiglevel==0.0) {
error("call mdist.option first");
return;
}
//compute the total length of the sequence
seqlen=0;
for (i=0; i<*nseq; i++) {
seqlen+=lseq[i]-Rpwm->nrow+1;
}
//init the maximal clump size and the max number of hits
maxclumpsize=(double)mclump[0];
maxhits=(double)mhit[0];
singlestranded=*sstrand;
delta=Calloc(Rpwm->nrow,double);
deltap=Calloc(Rpwm->nrow,double);
if (delta==NULL||deltap==NULL) {
error("Memory-allocation in Rcompoundpoisson_useBeta failed");
}
// initialize the extention factors
memset(extention, 0, 3*sizeof(double));
if (singlestranded==1) {
computeDeltasSingleStranded(delta, beta, Rpwm->nrow);
computeExtentionFactorsKoppSingleStranded(extention, beta, Rpwm->nrow);
theta=initThetaSingleStranded(maxclumpsize);
if (theta==NULL) {
error("Memory-allocation in initTheta failed");
}
computeInitialClumpKoppSingleStranded(theta, delta, Rpwm->nrow);
computeThetaSingleStranded(maxclumpsize, theta, extention, Rpwm->nrow);
lambda=computePoissonParameterSingleStranded(seqlen, Rpwm->nrow,
maxclumpsize, alpha[0],theta);
computeCompoundPoissonDistributionKempSingleStranded(lambda, maxhits,
maxclumpsize, theta, hitdistribution);
} else {
beta3p[0]=(beta3p[0]+EPSILON)/(1+2*EPSILON);
computeDeltas(delta, deltap, beta, beta3p,beta5p,Rpwm->nrow);
computeExtentionFactorsKopp(extention, delta, deltap, beta,
beta3p, beta5p, Rpwm->nrow);
theta=initTheta(maxclumpsize);
if (theta==NULL) {
error("Memory-allocation in initTheta failed");
}
computeInitialClumpKopp(theta, beta3p,delta, deltap, Rpwm->nrow);
computeTheta(maxclumpsize, theta, extention, Rpwm->nrow);
lambda=computePoissonParameter(seqlen, Rpwm->nrow, maxclumpsize,
alpha[0],theta);
computeCompoundPoissonDistributionKemp(lambda, maxhits, maxclumpsize,
theta, hitdistribution);
}
deleteTheta(theta);
Free(delta);
Free(deltap);
}
