void SetupAAMatrix()
{
int i,j,k;
double mr;
double sum;
double U[SQNUM_AA], V[SQNUM_AA], T1[SQNUM_AA], T2[SQNUM_AA];
k=0;
for (i=0; i<NUM_AA-1; i++) {
for (j=i+1; j<NUM_AA; j++) {
Qij[i*NUM_AA+j] = Qij[j*NUM_AA+i] = aaRelativeRate[k++];
}
}
for (i=0; i<NUM_AA; i++) {
for (j=0; j<NUM_AA; j++) {
Qij[i*NUM_AA+j] *= aaFreq[j];
}
}
mr=0;
for (i=0; i<NUM_AA; i++) {
sum = 0;
Qij[i*NUM_AA+i]=0;
for (j=0; j<NUM_AA; j++) {
sum += Qij[i*NUM_AA+j];
}
Qij[i*NUM_AA+i] = -sum;
mr += aaFreq[i] * sum;
}
abyx(1.0/mr, Qij, SQNUM_AA);
if ((k=eigen(1, Qij, NUM_AA, Root, T1, U, V, T2))!=0) {
fprintf(stderr, "\ncomplex roots in SetupAAMatrix");
exit(EXIT_FAILURE);
}
xtoy (U, V, SQNUM_AA);
matinv (V, NUM_AA, NUM_AA, T1);
for (i=0; i<NUM_AA; i++) {
for (j=0; j<NUM_AA; j++) {
for (k=0; k<NUM_AA; k++) {
Cijk[i*SQNUM_AA+j*NUM_AA+k] = U[i*NUM_AA+k]*V[k*NUM_AA+j];
}
}
}
}
double lfun (double x[], int np)
{
GaussLegendreRule(&xI, &wI, com.npoints);
for (Gtree=0; Gtree<com.nGtree;Gtree++){
for(igrid=0; igrid<K*K; igrid++){
if(Gtree==G1a||Gtree==G1b || Gtree==G1c){
if(com.model==M2SIM3s){
xtoy(Q,Q1,DIM*DIM);
complexroots (Q1, Pt1, t[0]*t[1]);
if(0 && igrid==0){
debug_print(Pt1, DIM);
}
xtoy(Q,Q1,DIM*DIM);
complexroots (Q1, Pt0, t[0]-t[0]*t[1]);
if(0 && igrid==0){
debug_print(Pt0, DIM);
}
if (Gtree==G1c){
}
else if (Gtree==G1b){
}
else if (Gtree==G1a){
}
}
b[1]=t[0]*t[1];
b[0]=t[0]-t[0]*t[1];
}
else if(Gtree==G2a || Gtree==G2b || Gtree==G2c || Gtree== G3a || Gtree ==G3b || Gtree ==G3c){
if(com.model==M2SIM3s){
xtoy(Q,Q1,DIM*DIM);
complexroots (Q1, Pt0, tau1-t[1]); /*ÔÚpt.cÀֱ½ÓÓÿÉÄÜÓÐÎÊÌâ*/
xtoy(Q,Q1,DIM*DIM);
complexroots (Q1, Pt1, t[1]);
//printf("\n In lfun after end2\n");
for(s=1;s<=8;s++){ //problems about s-1
if (Gtree==G2c || Gtree==G3c)
f[s-1]=(Pt1[get_ij(s,1,DIM)] * is2(11,Pt0,DIM) + Pt1[s,2,DIM]*is2(20,Pt0,DIM)) * 2/theta1
+ (Pt1[get_ij(s,7,DIM)] * is2(17,Pt0,DIM) + Pt1[s,8,DIM]*is2(14,Pt0,DIM)) * 2/theta2;
else if (Gtree==G2b || Gtree==G3b)
f[s-1]=(Pt1[get_ij(s,1,DIM)] * is2(10,Pt0,DIM) + Pt1[s,3,DIM]*is2(19,Pt0,DIM))*2/theta1
+(Pt1[get_ij(s,6,DIM)] * is2(16,Pt0,DIM) + Pt1[s,8,DIM]*is2(13,Pt0,DIM))*2/theta2;
else if (Gtree==G2a || Gtree==G3a)
f[s-1]=(Pt1[get_ij(s,1,DIM)] * is2( 9,Pt0,DIM) + Pt1[s,5,DIM]*is2(18,Pt0,DIM)) *2/theta1
+(Pt1[get_ij(s,4,DIM)] * is2(15,Pt0,DIM) + Pt1[s,8,DIM]*is2(12,Pt0,DIM)) *2/theta2;
}
}
if(Gtree==G2a || Gtree==G2b || Gtree==G2c){
g=exp(-t[0]);
for(s=1;s<=8;s++)
f[s-1]*=g;
b[1]=t[1];
b[0]= 2.0*t[0]/theta5+tau1-t[1];
}
else if(Gtree==G3a || Gtree==G3b || Gtree==G3c){
g= exp(-t[0])*exp(-2*(tau0-tau1)/theta5);
for(s=1;s<=8;s++)
f[s-1]*=g;
b[1]=t[1];
b[0]= 2.0*t[0]/theta4+tau0-t[1];
}
}
else{
//printf("\n In lfun after end3\n");
if (Gtree==G4a || Gtree==G4b || Gtree==G4c){
g= exp(-3*t[0]*t[1]-t[0]*(1-t[1]));
b[1]=theta5/2*t[0]*t[1]+tau1;
b[0]=theta5/2*t[0]+tau1-b[1];
}//above checked
else if (Gtree==G5a || Gtree==G5b || Gtree==G5c){
g=exp(-2*t[1]-t[0])* exp(-2.0*(tau0-tau1)/theta5);
b[1]=theta5/2*t[1]+tau1;
b[0]=theta4/2*t[0]+tau0-b[1];
}
else if (Gtree==G6a || Gtree==G6b || Gtree==G6c){
g= exp(-3*t[1]-t[0])* exp(-6.0*(tau0-tau1)/theta5);
b[1]=theta4/2*t[1]+tau0;
b[0]=theta4/2*(t[0]+t[1])+tau0-b[1];
} /*end else if*/
if(com.model==M2SIM3s){
xtoy(Q,Q1,DIM*DIM);
complexroots (Q1, Ptau1, tau1);
for(s=1;s<=8;s++)
f[s-1]= is3(s,Ptau1,DIM)*g;
}
}
for(s=0;s<8;s++)
{
com.wwprior[Gtree][igrid][s] = f[s] * com.wwprior[Gtree][igrid][0];
//printf("wwprior[%d][%d][%d]=%f ",Gtree, igrid,s,com.wwprior[Gtree][igrid][s]);
}
//printf("\n"); //hhh
if(!com.fix_locusrate)
p0124Fromb0b1(com.bp0124[Gtree]+igrid*5, b);
else {
com.bp0124[Gtree][igrid*2+0] = b[0];
com.bp0124[Gtree][igrid*2+1] = b[1];
}
/* printf("%-3s %5d y%9.5f%9.5f t%9.5f%9.5f b%9.5f%9.5f\n",
GtreeStr[Gtree], igrid+1, y[0],y[1], t[0],t[1], b[0],b[1]); */
//printf("In lfun after igrid loop !!!!\n"); zzz
}
for(locus=0; locus<com.ndata; locus++) {
Li = lnpD_locus(locus,com.state[locus]);
if(com.model==M1DiscreteBeta)
com.pDclass[itau1*com.ndata+locus] = Li;
else
lnL += Li;
n = com.Nij + locus*5;
if(debug) printf("%d\t%d\t%d\t%d\t%d\t%.6f\n", n[0],n[1],n[2],n[3],n[4], Li);
}
return(-lnL);
}
void RateMatrix::SetupMatrix(bool transition_probability_independent_sites_setup)
{
unsigned int i,j,k;
double mr;
double sum;
double U[numStates_squared+1], V[numStates_squared+1], T1[numStates_squared+1], T2[numStates_squared+1];
double Qij2pass[numStates_squared+1];
//////////
/// transition_probability_independent_sites_setup:
/// If we are calculating the transition probabilities as independent sites models, then we need
/// to run the code in the if statements. However, if we are doing the pseudo-dependent sites
/// calculations, we want to skip those code segments.
/// Segment #1:
/// * Sets the Qij entries to be the input substitution model.
/// -> For pseudo-dependent sites, we excise the Q matrix from the 4^N X 4^N sequence model.
/// Segment #2:
/// * Sets Qij so that branch length corresponds to expected number of changes.
/// -> pseudo-dependent sites branch lengths correspond not to 1 change per site, but whatever
/// the dependent sites model constrains it to.
//////////
CheckFrequencies();
k=0;
if (transition_probability_independent_sites_setup) {
for (i=0; i<numStates-1; i++) {
for (j=i+1; j<numStates; j++) {
Qij.at(i*numStates+j) = Qij.at(j*numStates+i) = Sij.at(k++);
}
}
for (i=0; i<numStates; i++) {
for (j=0; j<numStates; j++) {
Qij.at(i*numStates+j) *= pi.at(j);
}
}
mr=0;
for (i=0; i<numStates; i++) {
sum = 0;
Qij.at(i*numStates+i)=0;
for (j=0; j<numStates; j++) {
sum += Qij.at(i*numStates+j);
}
Qij.at(i*numStates+i) = -sum;
mr += pi.at(i) * sum;
}
//////////
/// Multiplies every element of Qij by 1.0/mr. This is abyx.
//////////
for (i=0; i<numStates_squared; Qij.at(i)*=1.0/mr,i++) ;
}
// Testcode: Print Qij.
//if (!transition_probability_independent_sites_setup) printQij();
//Testcode: does sum = 1?
sum = 0;
double partial = 0;
for (i = 0; i < numStates; i++) {
partial = 0;
for (j = 0; j < numStates; j++) {
if (i != j)
partial += Qij.at(i*numStates+j);
}
sum += pi.at(i) * partial;
}
//if (!transition_probability_independent_sites_setup) cerr << "Sum: " << sum << endl;
for (i = 0; i < numStates_squared; i++) Qij2pass[i]=Qij.at(i);
if ((k=eigen(1, Qij2pass, numStates, Root, T1, U, V, T2))!=0) {
fprintf(stderr, "\ncomplex roots in SetupMatrix");
exit(EXIT_FAILURE);
}
xtoy (U, V, numStates_squared);
matinv (V, numStates, numStates, T1);
vector<unsigned int> squared (numStates, 0), power_1 (numStates, 0);
for (i=0; i<numStates; i++) { squared[i]=i*numStates_squared; power_1[i]=i*numStates; }
for (i=0; i<numStates; i++) {
for (j=0; j<numStates; j++) {
for (k=0; k<numStates; k++) {
Cijk.at(squared[i]+power_1[j]+k) = U[power_1[i]+k]*V[power_1[k]+j];
}
}
}
}
int main(void) {
print_int10(xtoy(10, 2));
print_char('\n');
print_int10(xtoy(-100, 4));
return 0;
}