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optimiz.c
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/*
PHYML : a program that computes maximum likelihood phylogenies from
DNA or AA homologous sequences
Copyright (C) Stephane Guindon. Oct 2003 onward
All parts of the source except where indicated are distributed under
the GNU public licence. See http://www.opensource.org for details.
*/
#include "utilities.h"
#include "optimiz.h"
#include "ml.h"
#include "free.h"
#include "sigAnalyse.h"
double ROUND_MAX;
extern int stop_next_point;
/*********************************************************/
void Optimize_Single_Param_Generic(arbre *tree, double *param,
double start,
double lim_inf, double lim_sup,
int n_max_iter, double * lk_other_vec, int maximum)
{
double ax,bx,cx;
/* double fa,fb,fc; */
double lk_init;
lk_init = tree->tot_loglk;
tree->mod->s_opt->opt_bl =
tree->both_sides = 0;
ax = lim_inf;
if((*param < lim_inf) ||
(*param > lim_sup)) bx = (lim_sup-lim_inf)/2.;
else bx = start;
cx = lim_sup;
/* Generic_Brak(param, */
/* &ax,&bx,&cx, */
/* &fa,&fb,&fc, */
/* lim_inf, lim_sup, */
/* tree); */
Generic_Brent(param,
ax,bx,cx,1.e-10,
param,tree,n_max_iter, lk_other_vec, maximum);
if(tree->tot_loglk < lk_init-MIN_DIFF_LK)
{
printf("\n %.10f < %.10f --> diff=%.10f\n",
tree->tot_loglk,lk_init,
tree->tot_loglk-lk_init);
Exit("\n. Optimisation failed !\n");
}
}
/*********************************************************/
int Generic_Brak(double *param,
double *ax, double *bx, double *cx,
double *fa, double *fb, double *fc,
double lim_inf, double lim_sup,
arbre *tree, double * lk_other_vec, int maximum)
{
double ulim,u,r,q,fu,dum;
u = 0.0;
*param = *ax;
if(*param > lim_sup) *param = lim_sup;
if(*param < lim_inf) *param = lim_inf;
*fa=-Return_Lk(tree, lk_other_vec, maximum);
*param = *bx;
if(*param > lim_sup) *param = lim_sup;
if(*param < lim_inf) *param = lim_inf;
*fb=-Return_Lk(tree, lk_other_vec, maximum);
if (*fb > *fa) {
SHFT(dum,*ax,*bx,dum)
SHFT(dum,*fb,*fa,dum)
}
*cx=(*bx)+MNBRAK_GOLD*(*bx-*ax);
*param = fabs(*cx);
if(*param > lim_sup) *param = lim_sup;
if(*param < lim_inf) *param = lim_inf;
*fc=-Return_Lk(tree, lk_other_vec, maximum);
while (*fb > *fc)
{
if(*ax > lim_sup) *ax = lim_sup;
if(*ax < lim_inf) *ax = lim_inf;
if(*bx > lim_sup) *bx = lim_sup;
if(*bx < lim_inf) *bx = lim_inf;
if(*cx > lim_sup) *cx = lim_sup;
if(*cx < lim_inf) *cx = lim_inf;
if(u > lim_sup) u = lim_sup;
if(u < lim_inf) u = lim_inf;
r=(*bx-*ax)*(*fb-*fc);
q=(*bx-*cx)*(*fb-*fa);
u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
(2.0*SIGN(MAX(fabs(q-r),MNBRAK_TINY),q-r));
ulim=(*bx)+MNBRAK_GLIMIT*(*cx-*bx);
if ((*bx-u)*(u-*cx) > lim_inf)
{
*param = fabs(u);
if(*param > lim_sup) {*param = u = lim_sup;}
if(*param < lim_inf) {*param = u = lim_inf;}
fu=-Return_Lk(tree, lk_other_vec, maximum);
if (fu < *fc)
{
*ax=(*bx);
*bx=u;
*fa=(*fb);
*fb=fu;
(*ax)=fabs(*ax);
(*bx)=fabs(*bx);
(*cx)=fabs(*cx);
return(0);
}
else if (fu > *fb)
{
*cx=u;
*fc=fu;
(*ax)=fabs(*ax);
(*bx)=fabs(*bx);
(*cx)=fabs(*cx);
return(0);
}
u=(*cx)+MNBRAK_GOLD*(*cx-*bx);
*param = fabs(u);
if(*param > lim_sup) {*param = u = lim_sup;}
if(*param < lim_inf) {*param = u = lim_inf;}
fu=-Return_Lk(tree, lk_other_vec, maximum);
}
else if ((*cx-u)*(u-ulim) > lim_inf)
{
*param = fabs(u);
if(*param > lim_sup) {*param = u = lim_sup;}
if(*param < lim_inf) {*param = u = lim_inf;}
fu=-Return_Lk(tree, lk_other_vec, maximum);
if (fu < *fc)
{
SHFT(*bx,*cx,u,*cx+MNBRAK_GOLD*(*cx-*bx))
*param = fabs(u);
SHFT(*fb,*fc,fu,-Return_Lk(tree, lk_other_vec, maximum))
}
}
else if ((u-ulim)*(ulim-*cx) >= lim_inf)
{
u=ulim;
*param = fabs(u);
if(*param > lim_sup) {*param = u = lim_sup;}
if(*param < lim_inf) {*param = u = lim_inf;}
fu=-Return_Lk(tree, lk_other_vec, maximum);
}
else
{
u=(*cx)+MNBRAK_GOLD*(*cx-*bx);
*param = fabs(u);
if(*param > lim_sup) {*param = u = lim_sup;}
if(*param < lim_inf) {*param = u = lim_inf;}
fu=-Return_Lk(tree, lk_other_vec, maximum);
}
SHFT(*ax,*bx,*cx,u)
SHFT(*fa,*fb,*fc,fu)
}
(*ax)=fabs(*ax);
(*bx)=fabs(*bx);
(*cx)=fabs(*cx);
return(0);
}
/*********************************************************/
double Generic_Brent(double *param,
double ax, double bx, double cx, double tol,
double *xmin, arbre *tree, int n_iter_max, double * lk_other_vec, int maximum)
{
int iter;
double a,b,d,etemp,fu,fv,fw,fx,p,q,r,tol1,tol2,u,v,w,x,xm;
double e=0.0;
double init_loglk, max_loglk;
double bestx;
d=0.0;
a=((ax < cx) ? ax : cx);
b=((ax > cx) ? ax : cx);
x=w=v=bx;
*param=bx;
Lk(tree,tree->data, lk_other_vec, maximum);
fw=fv=fx=-tree->tot_loglk;
init_loglk = tree->tot_loglk;
max_loglk = UNLIKELY;
bestx = bx;
for(iter=1;iter<=BRENT_ITMAX;iter++)
{
xm=0.5*(a+b);
tol2=2.0*(tol1=tol*fabs(x)+BRENT_ZEPS);
if(fabs(x-xm) <= (tol2-0.5*(b-a)))
{
if(tree->tot_loglk < init_loglk - MIN_DIFF_LK)
{
printf("\n. WARNING : Brent failed\n");
*param = bestx;
Lk(tree,tree->data, lk_other_vec, maximum);
}
*xmin=x;
return -fx;
}
if(fabs(e) > tol1)
{
r=(x-w)*(fx-fv);
q=(x-v)*(fx-fw);
p=(x-v)*q-(x-w)*r;
q=2.0*(q-r);
if(q > 0.0) p = -p;
q=fabs(q);
etemp=e;
e=d;
if(fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
{
d=BRENT_CGOLD*(e=(x >= xm ? a-x : b-x));
/* printf("Golden section step\n"); */
}
else
{
d=p/q;
u=x+d;
if (u-a < tol2 || b-u < tol2)
d=SIGN(tol1,xm-x);
/* printf("Parabolic step\n"); */
}
}
else
{
d=BRENT_CGOLD*(e=(x >= xm ? a-x : b-x));
/* printf("Golden section step (default)\n"); */
}
u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
*param=u;
Lk(tree,tree->data, lk_other_vec, maximum);
fu=-tree->tot_loglk;
if(tree->tot_loglk > max_loglk)
{
max_loglk = tree->tot_loglk;
bestx = u;
}
/* printf("param=%f loglk=%f\n",*param,tree->tot_loglk); */
if(fu <= fx)
{
if(iter > n_iter_max)
{
if(tree->tot_loglk < init_loglk - MIN_DIFF_LK)
printf("\n. WARNING : Brent failed\n");
return tree->tot_loglk;
}
if(u >= x) a=x; else b=x;
SHFT(v,w,x,u)
SHFT(fv,fw,fx,fu)
}
else
{
if (u < x) a=u; else b=u;
if (fu <= fw || w == x)
{
v=w;
w=u;
fv=fw;
fw=fu;
}
else if (fu <= fv || v == x || v == w) {
v=u;
fv=fu;
}
}
}
Exit("\n. Too many iterations in BRENT !");
return(-1);
/* Not Reached ?? *xmin=x; */
/* Not Reached ?? return fx; */
}
/*********************************************************/
double RRparam_GTR_Golden(double ax, double bx, double cx, double tol,
double *xmin, arbre *tree, allseq *alldata, double *param, int n_iter_max, double * lk_other_vec, int maximum)
{
double f1,f2,x0,x1,x2,x3;
int n_iter;
x0=ax;
x3=cx;
if (fabs(cx-bx) > fabs(bx-ax))
{
x1=bx;
x2=bx+GOLDEN_C*(cx-bx);
}
else
{
x2=bx;
x1=bx-GOLDEN_C*(bx-ax);
}
(*param)=x1;
Lk(tree,alldata, lk_other_vec, maximum);
f1=-tree->tot_loglk;
(*param)=x2;
Lk(tree,alldata, lk_other_vec, maximum);
f2=-tree->tot_loglk;
n_iter = 0;
while (fabs(x3-x0) > tol*(fabs(x1)+fabs(x2)))
{
if (f2 < f1)
{
SHFT3(x0,x1,x2,GOLDEN_R*x1+GOLDEN_C*x3)
(*param)=x2;
Lk(tree,alldata, lk_other_vec, maximum);
SHFT2(f1,f2,-tree->tot_loglk)
}
else
{
SHFT3(x3,x2,x1,GOLDEN_R*x2+GOLDEN_C*x0)
(*param)=x1;
Lk(tree,alldata, lk_other_vec, maximum);
SHFT2(f2,f1,-tree->tot_loglk)
}
if(n_iter++ > n_iter_max) break;
/* printf("p=%E %f\n",(*param),tree->tot_loglk); */
}
if (f1 < f2)
{
*xmin=x1;
return f1;
}
else
{
*xmin=x2;
return f2;
}
}
/*********************************************************/
double Br_Len_Golden(double ax, double bx, double cx, double tol,
double *xmin, edge *b_fcus, arbre *tree, double * lk_other_vec, int maximum)
{
double f1,f2,x0,x1,x2,x3;
x0=ax;
x3=cx;
if (fabs(cx-bx) > fabs(bx-ax))
{
x1=bx;
x2=bx+GOLDEN_C*(cx-bx);
}
else
{
x2=bx;
x1=bx-GOLDEN_C*(bx-ax);
}
b_fcus->l=x1;
f1 = -Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum);
b_fcus->l=x2;
f2 = -Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum);
while (fabs(x3-x0) > tol*(fabs(x1)+fabs(x2)))
{
if (f2 < f1)
{
SHFT3(x0,x1,x2,GOLDEN_R*x1+GOLDEN_C*x3)
b_fcus->l=x2;
SHFT2(f1,f2,-Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum))
}
else
{
SHFT3(x3,x2,x1,GOLDEN_R*x2+GOLDEN_C*x0)
b_fcus->l=x1;
SHFT2(f2,f1,-Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum))
}
}
if (f1 < f2)
{
*xmin=fabs(x1);
return -f1;
}
else
{
*xmin=fabs(x2);
return -f2;
}
}
/*********************************************************/
int Br_Len_Brak(double *ax, double *bx, double *cx,
double *fa, double *fb, double *fc,
edge *b_fcus, arbre *tree, double * lk_other_vec, int maximum)
{
double ulim,u,r,q,fu,dum;
b_fcus->l = *ax;
*fa=-Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum);
b_fcus->l = *bx;
*fb=-Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum);
if (*fb > *fa) {
SHFT(dum,*ax,*bx,dum)
SHFT(dum,*fb,*fa,dum)
}
*cx=(*bx)+MNBRAK_GOLD*(*bx-*ax);
b_fcus->l = fabs(*cx);
*fc=-Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum);
while (*fb > *fc)
{
r=(*bx-*ax)*(*fb-*fc);
q=(*bx-*cx)*(*fb-*fa);
u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
(2.0*SIGN(MAX(fabs(q-r),MNBRAK_TINY),q-r));
ulim=(*bx)+MNBRAK_GLIMIT*(*cx-*bx);
if ((*bx-u)*(u-*cx) > 0.0)
{
b_fcus->l = fabs(u);
fu=-Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum);
if (fu < *fc)
{
*ax=(*bx);
*bx=u;
*fa=(*fb);
*fb=fu;
(*ax)=fabs(*ax);
(*bx)=fabs(*bx);
(*cx)=fabs(*cx);
return(0);
}
else if (fu > *fb)
{
*cx=u;
*fc=fu;
(*ax)=fabs(*ax);
(*bx)=fabs(*bx);
(*cx)=fabs(*cx);
return(0);
}
u=(*cx)+MNBRAK_GOLD*(*cx-*bx);
b_fcus->l = fabs(u);
fu=-Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum);
}
else if ((*cx-u)*(u-ulim) > 0.0)
{
b_fcus->l = fabs(u);
fu=-Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum);
if (fu < *fc)
{
SHFT(*bx,*cx,u,*cx+MNBRAK_GOLD*(*cx-*bx))
b_fcus->l = fabs(u);
SHFT(*fb,*fc,fu,-Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum))
}
}
else if ((u-ulim)*(ulim-*cx) >= 0.0)
{
u=ulim;
b_fcus->l = fabs(u);
fu=-Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum);
}
else
{
u=(*cx)+MNBRAK_GOLD*(*cx-*bx);
b_fcus->l = fabs(u);
fu=-Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum);
}
SHFT(*ax,*bx,*cx,u)
SHFT(*fa,*fb,*fc,fu)
}
(*ax)=fabs(*ax);
(*bx)=fabs(*bx);
(*cx)=fabs(*cx);
return(0);
}
/*********************************************************/
double Br_Len_Brent(double ax, double bx, double cx, double tol,
double *xmin, edge *b_fcus, arbre *tree, int n_iter_max, double * lk_other_vec, int maximum)
{
int iter;
double a,b,d,etemp,fu,fv,fw,fx,p,q,r,tol1,tol2,u,v,w,x,xm;
double e=0.0;
d=0.0;
a=((ax < cx) ? ax : cx);
b=((ax > cx) ? ax : cx);
x=w=v=bx;
b_fcus->l = fabs(bx);
fw=fv=fx=-Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum);
for(iter=1;iter<=BRENT_ITMAX;iter++)
{
xm=0.5*(a+b);
tol2=2.0*(tol1=tol*fabs(x)+BRENT_ZEPS);
if(fabs(x-xm) <= (tol2-0.5*(b-a)))
{
*xmin=x;
Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum);
return -fx;
}
if(fabs(e) > tol1)
{
r=(x-w)*(fx-fv);
q=(x-v)*(fx-fw);
p=(x-v)*q-(x-w)*r;
q=2.0*(q-r);
if(q > 0.0) p = -p;
q=fabs(q);
etemp=e;
e=d;
if(fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
d=BRENT_CGOLD*(e=(x >= xm ? a-x : b-x));
else{
d=p/q;
u=x+d;
if (u-a < tol2 || b-u < tol2)
d=SIGN(tol1,xm-x);
}
}
else
{
d=BRENT_CGOLD*(e=(x >= xm ? a-x : b-x));
}
u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
if(u<BL_MIN) u = BL_MIN;
b_fcus->l=fabs(u);
fu=-Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum);
/* printf("edge %d l=%f lnL=%f\n",b_fcus->num,b_fcus->l,fu); */
if(fu <= fx)
{
if(iter > n_iter_max)
{
printf("\n. WARNING : too many iterations in Brent\n");
b_fcus->l = fabs(bx);
Lk_At_Given_Edge(tree,b_fcus, lk_other_vec, maximum);
return tree->tot_loglk;
}
if(u >= x) a=x; else b=x;
SHFT(v,w,x,u)
SHFT(fv,fw,fx,fu)
}
else
{
if (u < x) a=u; else b=u;
if (fu <= fw || w == x)
{
v=w;
w=u;
fv=fw;
fw=fu;
}
else if (fu <= fv || v == x || v == w) {
v=u;
fv=fu;
}
}
}
printf("Too many iterations in BRENT");
return(-1);
/* Not Reached ?? *xmin=x; */
/* Not Reached ?? return fx; */
}
/*********************************************************/
int Dist_Seq_Brak(double *ax, double *bx, double *cx,
double *fa, double *fb, double *fc,
allseq *data, int numseq1, int numseq2,
model *mod)
{
double ulim,u,r,q,fu,dum;
double dist;
double lk,dlk,d2lk;
dist = *ax;
*fa=-Lk_Given_Two_Seq(data,numseq1,numseq2,dist,mod,&lk,&dlk,&d2lk);
dist = *bx;
*fb=-Lk_Given_Two_Seq(data,numseq1,numseq2,dist,mod,&lk,&dlk,&d2lk);
if (*fb > *fa) {
SHFT(dum,*ax,*bx,dum)
SHFT(dum,*fb,*fa,dum)
}
*cx=(*bx)+MNBRAK_GOLD*(*bx-*ax);
dist = fabs(*cx);
*fc=-Lk_Given_Two_Seq(data,numseq1,numseq2,dist,mod,&lk,&dlk,&d2lk);
while (*fb > *fc)
{
r=(*bx-*ax)*(*fb-*fc);
q=(*bx-*cx)*(*fb-*fa);
u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
(2.0*SIGN(MAX(fabs(q-r),MNBRAK_TINY),q-r));
ulim=(*bx)+MNBRAK_GLIMIT*(*cx-*bx);
if ((*bx-u)*(u-*cx) > 0.0)
{
dist = fabs(u);
fu=-Lk_Given_Two_Seq(data,numseq1,numseq2,dist,mod,&lk,&dlk,&d2lk);
if (fu < *fc)
{
*ax=(*bx);
*bx=u;
*fa=(*fb);
*fb=fu;
return(0);
}
else if (fu > *fb)
{
*cx=u;
*fc=fu;
return(0);
}
u=(*cx)+MNBRAK_GOLD*(*cx-*bx);
dist = fabs(u);
fu=-Lk_Given_Two_Seq(data,numseq1,numseq2,dist,mod,&lk,&dlk,&d2lk);
}
else if ((*cx-u)*(u-ulim) > 0.0)
{
dist = fabs(u);
fu=-Lk_Given_Two_Seq(data,numseq1,numseq2,dist,mod,&lk,&dlk,&d2lk);
if (fu < *fc)
{
SHFT(*bx,*cx,u,*cx+MNBRAK_GOLD*(*cx-*bx))
dist = fabs(u);
SHFT(*fb,*fc,fu,-Lk_Given_Two_Seq(data,numseq1,numseq2,dist,mod,&lk,&dlk,&d2lk))
}
}
else if ((u-ulim)*(ulim-*cx) >= 0.0)
{
u=ulim;
dist = fabs(u);
fu=-Lk_Given_Two_Seq(data,numseq1,numseq2,dist,mod,&lk,&dlk,&d2lk);
}
else
{
u=(*cx)+MNBRAK_GOLD*(*cx-*bx);
dist = fabs(u);
fu=-Lk_Given_Two_Seq(data,numseq1,numseq2,dist,mod,&lk,&dlk,&d2lk);
}
SHFT(*ax,*bx,*cx,u)
SHFT(*fa,*fb,*fc,fu)
}
return(0);
}
/*********************************************************/
double Dist_Seq_Brent(double ax, double bx, double cx, double tol,
double *xmin, allseq *data,
int numseq1, int numseq2, model *mod)
{
int iter;
double a,b,d,etemp,fu,fv,fw,fx,p,q,r,tol1,tol2,u,v,w,x,xm;
double e=0.0;
double dist;
double lk,dlk,d2lk;
d=0.0;
a=((ax < cx) ? ax : cx);
b=((ax > cx) ? ax : cx);
x=w=v=bx;
dist = fabs(bx);
fw=fv=fx=-Lk_Given_Two_Seq(data,numseq1,numseq2,dist,mod,&lk,&dlk,&d2lk);
for(iter=1;iter<=BRENT_ITMAX;iter++)
{
xm=0.5*(a+b);
tol2=2.0*(tol1=tol*fabs(x)+BRENT_ZEPS);
if(fabs(x-xm) <= (tol2-0.5*(b-a)))
{
*xmin=x;
return -fx;
}
if(fabs(e) > tol1)
{
r=(x-w)*(fx-fv);
q=(x-v)*(fx-fw);
p=(x-v)*q-(x-w)*r;
q=2.0*(q-r);
if(q > 0.0) p = -p;
q=fabs(q);
etemp=e;
e=d;
if(fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
d=BRENT_CGOLD*(e=(x >= xm ? a-x : b-x));
else{
d=p/q;
u=x+d;
if (u-a < tol2 || b-u < tol2)
d=SIGN(tol1,xm-x);
}
} else
{
d=BRENT_CGOLD*(e=(x >= xm ? a-x : b-x));
}
u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
dist=fabs(u);
fu=-Lk_Given_Two_Seq(data,numseq1,numseq2,dist,mod,&lk,&dlk,&d2lk);
if(fu <= fx) {
if(u >= x) a=x; else b=x;
SHFT(v,w,x,u)
SHFT(fv,fw,fx,fu)
}
else
{
if (u < x) a=u; else b=u;
if (fu <= fw || w == x)
{
v=w;
w=u;
fv=fw;
fw=fu;
}
else if (fu <= fv || v == x || v == w) {
v=u;
fv=fu;
}
}
}
printf("\n . BRENT method failed, trying Newton-Raphson");
return(+1.0);
/* Not Reached ?? *xmin=x; */
/* Not Reached ?? return fx; */
}
/*********************************************************/
double Optimize_Dist(model *mod, double init, allseq *twoseqs)
{
double d_infa,d_max,d_infb;
double lk_infa, lk_max, lk_infb, lk;
d_infa = 100.*BL_MIN;
d_max = init;
d_infb = 3.*init;
if(init <= BL_MIN) {d_infa = -BL_START; d_max = .0; d_infb = BL_START;}
lk_infa = lk_max = lk_infb = .0;
Dist_Seq_Brak(&d_infa, &d_max, &d_infb,
&lk_infa,&lk_max,&lk_infb,
twoseqs,0,1,mod);
lk = (double)Dist_Seq_Brent(d_infa,d_max,d_infb,
1.e-5,&d_max,twoseqs,0,1,mod);
if(lk > .0) return -1.0;
else return d_max;
}
/*********************************************************/
void Round_Optimize(arbre *tree, allseq *data, int write_int, int read_int, int maximum)//, int read_int_end)
{
int n_round,each, i;
double lk_old, lk_new;//, tol;
node *root;
double *lk_vec; //The likelihood vector of the tree
double *lk_other_vec; //The likelihood vector which is the sum of the other trees likelihoods
//Listening to the user signal 1 in case the server tells to stop the computations
check_sigusr2();
lk_vec=(double *)mCalloc(tree->data->crunch_len,sizeof(double));
lk_other_vec=(double *)mCalloc(tree->data->crunch_len,sizeof(double));
//Allocating the space for the matrix containing the tree likelihoods
tree->mod->all_lk_vec = (double **)mCalloc(tree->input->n_trees,sizeof(double *));
for (i=0;i<tree->input->n_trees;i++) {
tree->mod->all_lk_vec[i] = (double *)mCalloc(tree->data->crunch_len,sizeof(double));
}
lk_new = tree->tot_loglk;
lk_old = UNLIKELY;
n_round = 0;
each = 1;
// tol = 1.e-2;
root = tree->noeud[0];
tree->mod->s_opt->opt_bl = 0;
tree->both_sides = 1;
//Zeroing the auxiliary likelihood vector
For(i,data->crunch_len) {
lk_other_vec[i]=0.0;
}
Lk(tree, data, lk_other_vec, maximum);
//printf ("Client %d : Initial tree->tot_loglk : %f\n", getpid(), tree->tot_loglk);
For (i, tree->data->crunch_len) {
lk_vec[i]=tree->true_site_lk[i];
}
//Sending the initial likelihood vector
int wok = write(write_int,lk_vec, tree->data->crunch_len * sizeof(double));
if (wok == -1)
{
printf("PROBLEM WRITE in Simu\n");
exit(-1);
}//It is better if the read is blocking here
//We wait for the "go" from the server :
if (read(read_int, &i, sizeof(int))<sizeof(int)) {
printf("PROBLEM READ in Simu\n");
exit(-1);
}//It is better if the read is blocking here !
//USING THE FILE TO COMMUNICATE
if(tree->input->HMM) {
Read_From_Memory_With_Lambda (tree->input->fname, tree->mod->all_lk_vec, &tree->mod->hmm_lambda, tree->input->n_trees, tree->data->crunch_len);
}
else {
//printf ("Reading without lambda\n");
Read_From_Memory (tree->input->fname, tree->mod->all_lk_vec, tree->input->n_trees, tree->data->crunch_len);
}
Update_Lk_Vector_In_Lk_Table (tree);
lk_other_vec = Compute_Lk_Summary (tree, tree->mod->all_lk_vec, tree->input->n_trees, tree->input->maxi, tree->input->current_tree);
Lk(tree,data, lk_other_vec, maximum);
lk_new = lk_old = tree->tot_loglk;
// fcntl(read_int, F_SETFL, fcntl(read_int, F_GETFL) | O_NONBLOCK);//Read non blocking
// fcntl(write_int, F_SETFL, fcntl(write_int, F_GETFL) | O_NONBLOCK);//write non blocking
do
{
// printf("tree->tot_loglk before Optimize_Br_Len_Serie : %f\n",tree->tot_loglk);
(!((n_round+2)%2))?(root=tree->noeud[0]):(root=tree->noeud[tree->n_otu-1]);
Optimize_Br_Len_Serie(root,
root->v[0],
root->b[0],
tree,
data,
5, lk_other_vec, maximum);
tree->mod->s_opt->opt_bl = 0;
tree->both_sides = 1;
// printf("tree->tot_loglk After Optimize_Br_Len_Serie : %f -> %f->",lk_old, tree->tot_loglk);
Lk(tree,data, lk_other_vec, maximum);
// printf("AGAIN %f\n", tree->tot_loglk);
if(!each)
{
each = 1;
if(tree->mod->s_opt->print) printf("\n");
Optimiz_All_Free_Param(tree,tree->mod->s_opt->print, lk_other_vec, maximum);
tree->mod->s_opt->opt_bl = 0;
tree->both_sides = 1;
Lk(tree,data, lk_other_vec, maximum);
}
// printf("tree->tot_loglk AFTER2 opt : %f -> %f\n",lk_old, tree->tot_loglk);
lk_new = tree->tot_loglk;
if(tree->mod->s_opt->print)
{
/* if(lk_old < UNLIKELY+1)
//write(write_int, &(tree->tot_loglk), sizeof(double));
printf("\n. Log(lk) : * -> %15.6f ",lk_new);
else
printf("\n. Log(lk) : %15.6f -> %15.6f ",lk_old,lk_new);
//write(write_int, &(tree->tot_loglk), sizeof(double));
*/
fflush(NULL);
}
if(lk_new < lk_old - MIN_DIFF_LK) {
Exit("\n. Optimization failed ! (Round_Optimize)\n");
}
//if(fabs(lk_new - lk_old) < MIN_DIFF_LK) break;
//else
lk_old = lk_new;
n_round++;
each--;
//We could send our new likelihood vector here
//As well as receive the new one
For (i, tree->data->crunch_len) {
lk_vec[i]=tree->true_site_lk[i];
}
wok = write(write_int, lk_vec, tree->data->crunch_len*sizeof(double));
if (wok == -1)
{
printf("PROBLEM WRITE in Simu\n");
exit(-1);
}//It is better if the read is blocking here
//USING THE FILE TO COMMUNICATE
if(tree->input->HMM) {
Read_From_Memory_With_Lambda (tree->input->fname, tree->mod->all_lk_vec, &tree->mod->hmm_lambda, tree->input->n_trees, tree->data->crunch_len);
}
else {
Read_From_Memory (tree->input->fname, tree->mod->all_lk_vec, tree->input->n_trees, tree->data->crunch_len);
}
Update_Lk_Vector_In_Lk_Table (tree);
lk_other_vec = Compute_Lk_Summary (tree, tree->mod->all_lk_vec, tree->input->n_trees, tree->input->maxi, tree->input->current_tree);
Lk(tree,data, lk_other_vec, maximum);
lk_new = tree->tot_loglk;
lk_old=lk_new;
}
while(!stop_next_point);
if(tree->mod->s_opt->print) printf("\n");
Optimiz_All_Free_Param(tree,tree->mod->s_opt->print, lk_other_vec, maximum);
For (i, tree->data->crunch_len) {
lk_vec[i]=tree->true_site_lk[i];
}
wok = write(write_int, lk_vec, tree->data->crunch_len*sizeof(double));
free(lk_vec);
free(lk_other_vec);
}
/*********************************************************/
void Round_Optimize_End(arbre *tree, allseq *data, int write_int, int read_int, int maximum)
{
int n_round,each, i;
double lk_old, lk_new;//, tol;
node *root;
double *lk_vec; //The likelihood vector of the tree
double *lk_other_vec; //The likelihood vector which is the sum of the other trees likelihoods
lk_vec=(double *)mCalloc(tree->data->crunch_len,sizeof(double));
lk_other_vec=(double *)mCalloc(tree->data->crunch_len,sizeof(double));
lk_new = tree->tot_loglk;
lk_old = UNLIKELY;
n_round = 0;
each = 1;
// tol = 1.e-2;
root = tree->noeud[0];
tree->mod->s_opt->opt_bl = 0;
tree->both_sides = 1;
int readok = read(read_int, lk_other_vec, tree->data->crunch_len*sizeof(double));
if (readok == EOF)
{
printf("PROBLEM READ in Round_Optimize_End\n");
exit(-1);
}//It is better if the read is blocking here
Lk(tree,data, lk_other_vec, maximum);
lk_new = lk_old = tree->tot_loglk;
while(n_round < ROUND_MAX)
{
// printf("tree->tot_loglk before Optimize_Br_Len_Serie : %f\n",tree->tot_loglk);
(!((n_round+2)%2))?(root=tree->noeud[0]):(root=tree->noeud[tree->n_otu-1]);