void StructuredHexRaster::resize(size_t num_i, size_t num_j, size_t num_k)
{
m_NumI = num_i;
m_NumJ = num_j;
m_NumK = num_k;
computeDeltas();
// if(m_CellLink) {
// delete m_CellLink;
// }
// size_t num_cells = m_NumI * m_NumJ * m_NumK;
// m_CellLink = new List(num_cells, num_cells/10); /// @todo Our version of "List" sets a minimum increment
}
void StructuredHexRaster::setupAligned(real xo1, real yo1, real zo1, real xo2, real yo2, real zo2)
{
/** @todo Use a more general alignment method with trafo-matrix and internal coord system.
* I assume these are co-aligned here. */
m_Xo = xo1;
m_Yo = yo1;
m_Zo = zo1;
m_Uxo = xo2 - xo1;
m_Uyo = 0;
m_Uzo = 0;
countFlops(1);
m_Vxo = 0;
m_Vyo = yo2 - yo1;
m_Vzo = 0;
countFlops(1);
m_Wxo = 0;
m_Wyo = 0;
m_Wzo = zo2 - zo1;
countFlops(1);
// position relative to inertial system
vec3_t shift_inertial2this;
shift_inertial2this[0] = -m_Xo;
shift_inertial2this[1] = -m_Yo;
shift_inertial2this[2] = -m_Zo;
m_transformInertial2This.setVector(shift_inertial2this);
/// @todo rotation NOT implemented!!!
computeDeltas();
// Transformation t; /// @todo keep for compatibility
// t.setVector(vec3_t(xo1, yo1, zo1));
// setTransformation(t.inverse());
}
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);
}
