void main(){
float x[200],u1,u2,mle[10],mlenum,mleden,lm,mlm,mu[4],sig[4],z;
int n,i,j,k,c;
FILE *p, *q;
clrscr();
randomize();
p=fopen("C:/cprog/3bin.txt","r");
q=fopen("C:/cprog/3bout.txt","w");
fscanf(p, "%d", &n);
for(i=0; i<n ; i++)
fscanf(p, "%f%f", &mu[i], &sig[i]);
fprintf(q, "N\t-2Log(lm(x))\n\n");
for(i=0;i<40;i++){
c=0; mlenum=0.0; mleden=0.0; lm=0.0;
for(j=0;j<n;j+=2){
u1=(float)rand()/(RAND_MAX+1.0);
u2=(float)rand()/(RAND_MAX+1.0);
x[j]=(float)sqrt(-2*log(u1))*cos(2.0*3.1428*u2);
x[j+1]=(float)sqrt(-2*log(u1))*sin(2.0*3.1428*u2);
x[j]=2+sqrt(12)*x[j];
x[j+1]=2+sqrt(12)*x[j+1];
}
for(j=0;j<3;j++){
mle[c]=0.0;
for(k=0;k<3;k++){
mle[c]=(float)maxlike(x, mu[j], sig[k], n);
if(c==0){
mlenum=mle[c];
mleden=mle[c];
}
else mleden=(float)max(mleden,mle[c]);
if((mu[j]==1 || mu[j]==2) && (sig[k]==4||sig[k]==9) && c>0)
mlenum=(float)max(mlenum,mle[c]);
}
c++;
}
lm=-2*(mlenum-mleden);
fprintf(q,"%d\t%f\n",i+1,lm);
mlm+=lm;
}
mlm=mlm/40;
z=(mlm-2)/sqrt(4);
if(z>1.95996 || z<-1.95996)
fprintf(q,"\n\nz = %f\n -2log(lm(x)) does not follow a chi-sq distribution with 2 d.f.",z);
else fprintf(q,"\n\nz = %f -2log(lm(x)) follows a chi-sq distribution with 2 d.f.",z);
fclose(p);
fclose(q);
}
int main(int argc, char** argv){
/* A->0 ; C->1 ; G->2 ; T->3 */
int i, j, nbseq, nbseqvrai, nbtree, nbdataset, maxtreesize, allcouples=0;
char nomfinseq[100], nomfintree[100], nomfopt[100], *seq[MAXNSP*MAXDATASET], *seqname[MAXNSP*MAXDATASET], *comments[MAXNSP*MAXDATASET], muet, print1;
char* alltrees, **c_tree, *prov, *prov2, *ctree1, *ctree2;
double **maxl;
FILE *treefile, *optfile, *outfile1, *outfile2, *in;
FILE* dutheil;
options opt;
/* printmemory_init(); */
init_cas();
srand48(seed);
/** input sequences **/
if(argc<2){
muet=0;
while(1){
printf("\nSequence file (MASE) ? ");
gets(nomfinseq);
in=fopen(nomfinseq, "r");
if(in) break;
printf("Cannot find file : %s\n", nomfinseq);
}
}
else{
in=fopen(argv[1], "r");
if(!in){
printf("Cannot find sequence file : %s\n", argv[1]);
exit(EXIT_FAILURE);
}
sprintf(nomfinseq, "%s", argv[1]);
muet=1;
}
fclose(in);
if(muet)
nbseq=readmasemuet(nomfinseq, seq, seqname, comments, MAXDATASET*MAXNSP);
else
nbseq=readmaseseqs(nomfinseq, seq, seqname, comments, MAXDATASET*MAXNSP);
nbseqvrai=nbseq;
for(i=1;i<=nbseq/2;i++){
if(strncmp(comments[i], ";;", 2)==0){
nbseqvrai=i;
break;
}
}
if(nbseq%nbseqvrai!=0){
printf("Bad sequence file %s\n", nomfinseq);
exit(EXIT_FAILURE);
}
nbdataset=nbseq/nbseqvrai;
for(i=0;i<nbdataset;i++)
refresh(seq+i*nbseqvrai, nbseqvrai, 0);
/** input trees **/
maxtreesize=50*nbseqvrai*MAXNTREE;
alltrees=(char*)check_alloc(maxtreesize+1, sizeof(char));
c_tree=(char**)check_alloc(MAXNTREE, sizeof(char*));
if(argc<3){
while(1){
printf("\nTree file ? ");
gets(nomfintree);
treefile=fopen(nomfintree, "r");
if(treefile) break;
printf("Cannot find file : %s\n", nomfintree);
}
}
else{
treefile=fopen(argv[2], "r");
if(!treefile){
printf("Cannot find tree file : %s\n", argv[2]);
exit(EXIT_FAILURE);
}
}
i=0;
while(i<maxtreesize && (alltrees[i]=getc(treefile))!=EOF) i++;
alltrees[i]='\0';
fclose(treefile);
i=0;
prov=alltrees;
while(*prov) {if(*prov==';') i++; prov++;}
free(c_tree);
c_tree=(char**)check_alloc(i, sizeof(char*));
i=0; prov=alltrees;
while(*prov){
if(*prov=='[') i++;
if(*prov==']') i--;
if(i!=0 && i!=1){
printf("Unmatched brackets [] in tree file\n");
exit(EXIT_FAILURE);
}
if(i==1 && (*prov==';' || *prov=='(')) *prov='.';
prov++;
}
nbtree=0;
prov=alltrees;
while(1){
prov2=strtok(prov, ";");
if(prov) prov=NULL;
if(!prov2) break;
while(*prov2 && *prov2!='(') prov2++;
if(*prov2==0) continue;
c_tree[nbtree]=prov2;
nbtree++;
}
for(i=0;i<nbtree;i++){
prov=c_tree[i];
while(*prov) prov++;
*prov=';'; *(prov+1)=0;
}
/** input options **/
if(argc<4){
while(1){
printf("\nOption file ? ");
gets(nomfopt);
optfile=fopen(nomfopt, "r");
if(optfile) break;
printf("Cannot find file : %s\n", nomfopt);
}
}
else{
optfile=fopen(argv[3], "r");
if(!optfile){
printf("Cannot find option file : %s\n", argv[3]);
exit(EXIT_FAILURE);
}
}
getoptions(&opt, optfile);
print1=opt->print->PRINT1;
allcouples=opt->ALLCOUPLES;
if(opt->print->EVAL_OUT){
dutheil=fopen("detailed_out", "w");
fprintf(dutheil, "numero\tarbre\tlnL\tTs/Tv\tGCanc\talpha\tcovar\tpi\n");
fclose(dutheil);
}
if(print1)
printf("\n%d sequence data sets and %d trees found : ", nbdataset, nbtree);
if(!allcouples){
nbdataset=mini(nbdataset, nbtree);
nbtree=nbdataset;
}
if(print1)
printf("%d evaluations processed\n\n", allcouples?nbdataset*nbtree:nbdataset);
maxl=(double**)check_alloc(nbdataset, sizeof(double*));
for(i=0;i<nbdataset;i++)
maxl[i]=(double*)check_alloc(nbtree, sizeof(double));
ctree1=(char*)check_alloc(50*nbseq, sizeof(char));
ctree2=(char*)check_alloc(50*nbseq, sizeof(char));
outfile1=fopen("treefile.eqgc", "w");
outfile2=fopen("treefile.ndgc", "w");
if(outfile1==NULL || outfile2==NULL){ printf("Cannot write tree file\n"); exit(EXIT_FAILURE); }
for(i=0;i<nbdataset;i++){
for(j=0;j<nbtree;j++){
if(!allcouples) j=i;
if(print1) printf("\ndata set %d , tree %d\n", i+1, j+1);
maxl[i][j]=maxlike(nbseqvrai, seq+i*nbseqvrai, seqname+i*nbseqvrai, c_tree[j], opt, ctree1, ctree2);
if(nbdataset*nbtree>1){
fprintf(outfile1, "[data set %d, tree %d]\n%s\n\n", i+1, j+1, ctree1);
fprintf(outfile2, "[data set %d, tree %d]\n%s\n\n", i+1, j+1, ctree2);
}
else{
fprintf(outfile1, "%s\n", ctree1);
fprintf(outfile2, "%s\n", ctree2);
}
if(!allcouples) break;
}
}
if(print1){
if(nbdataset*nbtree==1){
printf("Tree is written into files : treefile.eqgc (equilibrium G+C content)\n");
printf(" treefile.ndgc (G+C content at each node)\n\n");
}
else{
printf("Trees are written into files : treefile.eqgc (equilibrium G+C content)\n");
printf(" treefile.ndgc (G+C content at each node)\n\n");
}
}
return 0;
}
double shake(int nb, char** seq, char** seqname, char* ctree, options opt, char** eval_input, int nb_eval_input){
int nb2, i, j, ii, jj, k, l, *ttree[MAXNSP], **curtree, **newtree, **evaltree, nbbi, nbdclade, nbgclade, print1, print2;
int nochange, pres_grossiere=-1, l1, l2, restart_d, restart_g, oldmovedist;
int **dclade, **gclade, **newdclade, **newgclade, **ddist, **gdist, movedist, maxmovedist;
int **list_tree, lliste, *solid;
long nblist, nblistmax;
double *lgbp, *sortedlgbp, *lgbi, *bootvals, fracroot1, lkh, maxlkh, maxlcrossedbranch;
char *nom[MAXNSP], *nom2[MAXNSP], **dcladename, **gcladename, **list1, **list2, racine, *ctreenew, *ctreenew_nobl, *treedeb, *ctree1, *ctree2;
FILE* outfile1, *outfile2;
print_option trueprint, noprint;
print1=opt->print->PRINT1;
print2=opt->print->PRINT2;
noprint=check_alloc(1, sizeof(struct print_option));
noprint->PRINT3=0;
if(opt->print->PRINT2)
noprint->PRINT1=noprint->PRINT2=1;
else
noprint->PRINT1=noprint->PRINT2=0;
if(print1) noprint->PRINT0=1; else noprint->PRINT0=0;
trueprint=opt->print;
opt->print=noprint;
maxlcrossedbranch=opt->SH_MAXLCROSSED;
/* READ TREE STRING */
lgbp=(double*)check_alloc(nb+1, sizeof(double));
sortedlgbp=(double*)check_alloc(nb+1, sizeof(double));
lgbi=(double*)check_alloc(nb+1, sizeof(double));
for(i=0;i<nb+1;i++)
lgbp[i]=lgbi[i]=-1.;
solid=(int*)check_alloc(nb+1, sizeof(int));
bootvals=(double*)check_alloc(nb+1, sizeof(double));
if(nb>=MAXNSP) {printf("Too many sequences\n"); exit(EXIT_FAILURE);}
for(i=0;i<=nb;i++){
nom[i]=(char*)check_alloc(MAXLNAME+1, sizeof(char));
nom2[i]=(char*)check_alloc(MAXLNAME+1, sizeof(char));
ttree[i]=(int*)check_alloc(nb, sizeof(int));
}
list1=check_alloc(nb, sizeof(char*));
list2=check_alloc(nb, sizeof(char*));
curtree=(int**)check_alloc(nb+1, sizeof(int*));
newtree=(int**)check_alloc(nb+1, sizeof(int*));
evaltree=(int**)check_alloc(nb+1, sizeof(int*));
for(i=0;i<nb+1;i++) newtree[i]=(int*)check_alloc(nb-2, sizeof(int));
ctreenew=(char*)check_alloc(2*MAXLNAME*nb, sizeof(char));
ctree1=(char*)check_alloc(2*MAXLNAME*nb, sizeof(char));
ctree2=(char*)check_alloc(2*MAXLNAME*nb, sizeof(char));
ctreenew_nobl=(char*)check_alloc(2*MAXLNAME*nb, sizeof(char));
nb2=ctot(ctree, ttree, lgbi, lgbp, bootvals, nom, &racine, &nbbi);
if(nb2<nb){
printf("More species in sequence file than in tree file\n");
exit(EXIT_FAILURE);
}
if(nb2>nb){
printf("More species in tree file than in sequence file\n");
exit(EXIT_FAILURE);
}
/* PREPARE TREE : UNROOT, SET LEFT and RIGHT LISTS, SORT TAXA */
if(racine=='r'){
unroot(ttree, nb, lgbi, lgbp, bootvals, nom, list1, list2, &l1, &l2, &fracroot1);
}
else{
printf("Tree must be rooted\n");
exit(EXIT_FAILURE);
}
nbbi--;
if(nbbi!=nb-3){
printf("Tree must be bifurcating\n");
exit(EXIT_FAILURE);
}
for(i=0;i<nb;i++){
for(j=0;j<nb;j++){
if(samename(seqname[i], nom[j])){
curtree[i]=ttree[j];
sortedlgbp[i]=lgbp[j];
break;
}
}
}
for(i=0;i<nb-3;i++) if(bootvals[i]>opt->SH_MAXBOOTCROSSED) solid[i]=1;
ctree_noblbs(ctree, ctreenew_nobl, strlen(ctree));
/* EVALUATE INITIAL TREE */
if(print1)
printf("\nEvaluating initial tree : \n%s\n", ctreenew_nobl);
if(print2)
printf("\n");
maxlkh=maxlike(nb, seq, seqname, curtree, lgbi, sortedlgbp, nbbi, l1, list1, l2, list2, opt, NULL, NULL, NULL);
if(opt->SH_RESTART) save_current_best("current_best_tree", ctreenew_nobl, maxlkh, 1);
if(opt->SH_RESTART) save_evaluated("evaluated_trees", ctreenew_nobl, maxlkh, 1);
/* ALLOCATE SHAKE VARIABLES */
nbdclade=2*l1-1;
nbgclade=2*l2-1;
dclade=(int**)check_alloc(nbdclade, sizeof(int*));
for(i=0;i<nbdclade;i++)
dclade[i]=(int*)check_alloc(nb, sizeof(int));
gclade=(int**)check_alloc(2*nb, sizeof(int*));
for(i=0;i<nbgclade;i++)
gclade[i]=(int*)check_alloc(nb, sizeof(int));
newdclade=(int**)check_alloc(nbdclade, sizeof(int*));
for(i=0;i<nbdclade;i++)
newdclade[i]=(int*)check_alloc(nb, sizeof(int));
newgclade=(int**)check_alloc(nbgclade, sizeof(int*));
for(i=0;i<nbgclade;i++)
newgclade[i]=(int*)check_alloc(nb, sizeof(int));
ddist=(int**)check_alloc(nbdclade, sizeof(int*));
gdist=(int**)check_alloc(nbgclade, sizeof(int*));
for(i=0;i<nbdclade;i++) ddist[i]=(int*)check_alloc(nbdclade, sizeof(int));
for(i=0;i<nbgclade;i++) gdist[i]=(int*)check_alloc(nbgclade, sizeof(int));
dcladename=(char**)check_alloc(nbdclade, sizeof(char*));
gcladename=(char**)check_alloc(nbgclade, sizeof(char*));
for(i=0;i<nbdclade;i++)
dcladename[i]=(char*)check_alloc(nb*(MAXLNAME+3)+1, sizeof(char));
for(i=0;i<nbgclade;i++)
gcladename[i]=(char*)check_alloc(nb*(MAXLNAME+3)+1, sizeof(char));
nblistmax=nb*nb;
if(nblistmax<MIN_NBLISTMAX) nblistmax=MIN_NBLISTMAX;
if(nblistmax<nb_eval_input) nblistmax=nb_eval_input;
if(nblistmax>MAX_NBLISTMAX) nblistmax=MAX_NBLISTMAX;
while(1){
lliste=(nblistmax*(nb-3)+lmot-1)/lmot;
list_tree=(int**)check_alloc(nb, sizeof(int*));
for(i=0;i<nb;i++)
list_tree[i]=(int*)calloc(lliste, sizeof(int));
if(list_tree[nb-1]) break;
nblistmax/=2;
if(nblistmax==0){
printf("Not enough memory\n");
exit(EXIT_FAILURE);
}
}
/* SET LIST OF EVALUATED TREES */
if(eval_input){
nblist=0;
for(k=0;k<nb_eval_input;k++){
for(i=0;i<=nb;i++) ttree[i]=check_alloc(nb, sizeof(int));
nb2=ctot(eval_input[k], ttree, NULL, NULL, NULL, nom2, &racine, NULL);
if(racine=='r')
unroot(ttree, nb, NULL, NULL, NULL, nom2, NULL, NULL, NULL, NULL, NULL);
else{ printf("Evaluated trees must be rooted\n"); exit(EXIT_FAILURE);}
for(i=0;i<nb;i++){
for(j=0;j<nb;j++){
if(samename(seqname[i], nom2[j])){
evaltree[i]=ttree[j];
break;
}
}
}
if(deja_evalue(evaltree, nb, list_tree, nblist, nblistmax)) continue;
addtolist(evaltree, nb, list_tree, nblist, nblistmax);
nblist++;
}
printf("%d already evaluated topologies loaded\n", nblist);
}
else{
addtolist(curtree, nb, list_tree, 0, nblistmax);
nblist=1;
}
/* SHAKE */
treedeb=ctreenew;
nochange=1; movedist=0;
if(opt->SH_G>0 && opt->SH_G<nb-3)
maxmovedist=opt->SH_G;
else
maxmovedist=nb-3;
if(print1)
printf("\nStarting rearrangements\n");
do{
oldmovedist=movedist;
if(nochange==1) movedist++;
else movedist=1;
if(print1 && !(nochange==0 && oldmovedist==1)){
printf("\nCrossing %d internal branch", movedist);
if(movedist>1) printf("es");
printf("\n");
}
nochange=1;
while(1){
setclades(curtree, nb, seqname, l1, list1, l2, list2, dclade, gclade, ddist, gdist, nbdclade, nbgclade, dcladename, gcladename);
restart_d=0;
for(i=0;i<nbdclade;i++){
for(j=0;j<nbdclade;j++){
if(abs(ddist[i][j])!=movedist) continue;
if(ddist[i][j]<0) continue;
moveclade(dclade, newdclade, nbdclade, nb, ddist, i, j);
settree(newdclade, nbdclade, gclade, nbgclade, nb, newtree);
if(deja_evalue(newtree, nb, list_tree, nblist, nblistmax))
continue;
if(solid_branch_crossed(newtree, curtree, nb, solid))
continue;
addtolist(newtree, nb, list_tree, nblist, nblistmax);
nblist++;
if(print1){
printf("\nMoving %s toward %s\n", dcladename[i], dcladename[j]);
}
if(print2)
printf("\n");
lkh=maxlike(nb, seq, seqname, newtree, NULL, NULL, nbbi, l1, list1, l2, list2, opt, ctreenew, NULL, NULL);
if(lkh>maxlkh){
ctree_noblbs(ctreenew, ctreenew_nobl, strlen(ctreenew));
if(print1)
printf("New tree is optimal : \n%s\n\nRestarting rearrangements\n", ctreenew_nobl);
maxlkh=lkh;
copytree(newtree, curtree, nb);
if(opt->SH_RESTART) save_current_best("current_best_tree", ctreenew_nobl, lkh, 0);
if(opt->SH_RESTART) save_evaluated("evaluated_trees", ctreenew_nobl, lkh, 0);
restart_d=1;
nochange=0;
ctreenew=treedeb;
while(*ctreenew) {*ctreenew=0; ctreenew++; }
ctreenew=treedeb;
break;
}
else{
if(print1)
printf("No improvement:\n");
ctree_noblbs(ctreenew, ctreenew_nobl, strlen(ctreenew));
if(print1)
printf("%s\n", ctreenew_nobl);
if(opt->SH_RESTART) save_evaluated("evaluated_trees", ctreenew_nobl, lkh, 0);
}
ctreenew=treedeb;
while(*ctreenew) {*ctreenew=0; ctreenew++; }
ctreenew=treedeb;
}
if(restart_d) break;
}
if(!restart_d || movedist>1) break;
}
if(restart_d && movedist>1) continue;
while(1){
setclades(curtree, nb, seqname, l1, list1, l2, list2, dclade, gclade, ddist, gdist, nbdclade, nbgclade, dcladename, gcladename);
restart_g=0;
for(i=0;i<nbgclade;i++){
for(j=0;j<nbgclade;j++){
if(abs(gdist[i][j])!=movedist) continue;
if(gdist[i][j]<0) continue;
moveclade(gclade, newgclade, nbgclade, nb, gdist, i, j);
settree(dclade, nbdclade, newgclade, nbgclade, nb, newtree);
if(deja_evalue(newtree, nb, list_tree, nblist, nblistmax))
continue;
if(solid_branch_crossed(newtree, curtree, nb, solid))
continue;
addtolist(newtree, nb, list_tree, nblist, nblistmax);
nblist++;
if(print1){
printf("\nMoving %s toward %s\n", gcladename[i], gcladename[j]);
}
if(print2){
printf("\n");
}
lkh=maxlike(nb, seq, seqname, newtree, NULL, NULL, nbbi, l1, list1, l2, list2, opt, ctreenew, NULL, NULL);
if(lkh>maxlkh){
ctree_noblbs(ctreenew, ctreenew_nobl, strlen(ctreenew));
if(print1)
printf("New tree is optimal : \n%s\n\nRestarting rearrangements\n", ctreenew_nobl);
maxlkh=lkh;
copytree(newtree, curtree, nb);
if(opt->SH_RESTART) save_current_best("current_best_tree", ctreenew_nobl, lkh, 0);
if(opt->SH_RESTART) save_evaluated("evaluated_trees", ctreenew_nobl, lkh, 0);
restart_g=1;
nochange=0;
ctreenew=treedeb;
while(*ctreenew) {*ctreenew=0; ctreenew++; }
ctreenew=treedeb;
break;
}
else{
if(print1)
printf("No improvement:\n");
ctree_noblbs(ctreenew, ctreenew_nobl, strlen(ctreenew));
if(print1)
printf("%s\n", ctreenew_nobl);
if(opt->SH_RESTART) save_evaluated("evaluated_trees", ctreenew_nobl, lkh, 0);
}
ctreenew=treedeb;
while(*ctreenew) {*ctreenew=0; ctreenew++; }
ctreenew=treedeb;
}
if(restart_g) break;
}
if(!restart_g || movedist>1) break;
}
} while(nochange==0 || movedist!=maxmovedist);
/* FINAL EVALUATION */
if(print1)
printf("\nFinal evaluation\n");
if(print2)
printf("\n");
opt->print=trueprint;
maxlkh=maxlike(nb, seq, seqname, curtree, NULL, NULL, nbbi, l1, list1, l2, list2, opt, NULL, ctree1, ctree2);
if(ctree1){
outfile1=fopen("treefile.eqgc", "w");
outfile2=fopen("treefile.ndgc", "w");
if(outfile1==NULL || outfile2==NULL){ printf("Cannot write tree file\n"); exit(EXIT_FAILURE); }
fprintf(outfile1, "%s\n", ctree1);
fprintf(outfile2, "%s\n", ctree2);
if(print1){
printf("Tree is written into files : treefile.eqgc (equilibrium G+C content)\n");
printf(" treefile.ndgc (G+C content at each node)\n\n");
}
}
free(lgbp); free(sortedlgbp); free(lgbi);
free(bootvals);
for(i=0;i<nb;i++){ free(nom[i]); free(ttree[i]); }
free(list1); free(list2); free(curtree);
return maxlkh;
}
