void WatchDiamondWidget::set_height()
{
QPushButton* bt = qobject_cast<QPushButton*>(sender());
QDoubleSpinBox* sp = qobject_cast<QDoubleSpinBox*>(sender());
if(bt == bt_getDiamondZ){
sp_getDiamondZ->setValue(axisPos[2]);
set_var_param(3308,0);
}
else if(bt == bt_setDiamondZ){
sp_setDiamondZ->setValue(axisPos[2]);
set_var_param(3309,0);
}
else if(bt == bt_setGlueZ){
sp_setGlueZ->setValue(axisPos[2]);
set_var_param(3310,0);
}
else if(sp == sp_getDiamondZ){
set_var_param(3308,sp->value());
}
else if(sp == sp_setDiamondZ){
set_var_param(3309,sp->value());
}
else if(sp == sp_setGlueZ){
set_var_param(3310,sp->value());
}
}
double maxlike(int nbseq, char** seq, char** seqname, char* c_tree, options opt, char* ctree1, char* ctree2){
int i, j, k, l, ii, nbseq2, lgseq, lgsite, *drapeau, *drapeau2, cont=0, tree_is_rooted, nbparam, nbvrai, nbcompute, bl;
char **orderedseq, racine, *site;
double *lgbi, *lgbp, *weight, lkh, maxlkh=-1.e100, prov, rem_titv, rem_root, *freq;
static int nbtree=0;
FILE* outfile;
/* printmemory("deb maxlike"); */
gamma_nbcl=opt->init->GAMMA_NCL;
/* READ TREE, GET NB OF TAXA */
s_tree=(tree*)check_alloc(1, sizeof(tree));
lgseq=(int)strlen(seq[0]);
s_tree->alivebr=(int*)check_alloc(2*nbseq, sizeof(int));
s_tree->node=ctos(c_tree, &nbseq2, &tree_is_rooted);
if(strchr(c_tree, ':')) bl=1; else bl=0;
if (nbseq2>nbseq) {
printf("More taxa in tree file than in sequence file\n");
exit(EXIT_FAILURE);
}
/* ALLOCATE AND INIT S_TREE */
s_tree->nbseq=nbseq=nbseq2;
s_tree->seq=seq;
s_tree->names=seqname;
s_tree->listgc=(double*)check_alloc(2*nbseq, sizeof(double));
s_tree->listbr=(branche*)check_alloc(2*nbseq, sizeof(branche));
s_tree->lgbr_init=(double*)check_alloc(2*nbseq-3, sizeof(double));
for(i=0;i<2*nbseq-2;i++){
s_tree->listbr[i]=(struct branche*)check_alloc(1, sizeof(struct branche));
}
makelistbr_unrooted(NULL, s_tree->node[0], s_tree->listbr, s_tree->alivebr, 2*nbseq-3);
for(i=0;i<2*nbseq-3;i++) s_tree->lgbr_init[i]=s_tree->listbr[i]->length;
for(ii=0;ii<2*nbseq-3;ii++) s_tree->alivebr[ii]=1;
s_tree->nbalivebr=0;
for(i=0;i<2*nbseq-3;i++) s_tree->nbalivebr+=s_tree->alivebr[i];
set_var_param(s_tree, opt->compute);
nbparam=s_tree->nb_var_param;
s_tree->classlike_s=(double**)check_alloc(gamma_nbcl, sizeof(double));
for(i=0;i<gamma_nbcl;i++)
s_tree->classlike_s[i]=(double*)check_alloc(lgseq, sizeof(double));
s_tree->like_s=(double*)check_alloc(lgseq, sizeof(double));
s_tree->likeasrv_s=(double*)check_alloc(lgseq, sizeof(double));
s_tree->dlike_s=(double**)check_alloc(nbparam, sizeof(double*));
s_tree->dlikeasrv_s=(double**)check_alloc(nbparam, sizeof(double*));
for(i=0;i<nbparam;i++){
s_tree->dlike_s[i]=(double*)check_alloc(lgseq, sizeof(double));
s_tree->dlikeasrv_s[i]=(double*)check_alloc(lgseq, sizeof(double));
}
s_tree->d2like_s=(double**)check_alloc(nbparam, sizeof(double*));
s_tree->d2likeasrv_s=(double**)check_alloc(nbparam, sizeof(double*));
for(i=0;i<nbparam;i++){
s_tree->d2like_s[i]=(double*)check_alloc(lgseq, sizeof(double));
s_tree->d2likeasrv_s[i]=(double*)check_alloc(lgseq, sizeof(double));
}
s_tree->classdlike_s=(double***)check_alloc(gamma_nbcl, sizeof(double**));
s_tree->classd2like_s=(double***)check_alloc(gamma_nbcl, sizeof(double**));
for(i=0;i<gamma_nbcl;i++){
s_tree->classdlike_s[i]=(double**)check_alloc(nbparam, sizeof(double*));
s_tree->classd2like_s[i]=(double**)check_alloc(nbparam, sizeof(double*));
for(j=0;j<nbparam;j++){
s_tree->classdlike_s[i][j]=(double*)check_alloc(lgseq, sizeof(double));
s_tree->classd2like_s[i][j]=(double*)check_alloc(lgseq, sizeof(double));
}
}
s_tree->deriv=(double*)check_alloc(nbparam, sizeof(double));
s_tree->deriv2=(double*)check_alloc(nbparam, sizeof(double));
/* printmemory("fin tree alloc"); */
for(i=0;i<2*nbseq-2;i++)
alloc_node(s_tree->node[i], lgseq, nbparam, nbseq, (i<nbseq), 0, gamma_nbcl);
alloc_node(root, lgseq, nbparam, nbseq, 0, 0, gamma_nbcl);
/* printmemory("fin node alloc"); */
/* INIT LIKELIHOOD AT TIPS */
for(i=0;i<nbseq;i++){
for(j=0;j<4;j++){ /* 4 patterns for tip nodes */
for(k=0;k<4;k++){ /* 4 possible states */
for(l=0;l<gamma_nbcl;l++){
if(j==k) s_tree->node[i]->x[l][j][k]=1.;
else s_tree->node[i]->x[l][j][k]=0.;
}
}
}
}
/* CHECK SEQUENCE FILE */
for(i=nbseq2;i<2*nbseq2-2;i++) sprintf(s_tree->node[i]->nom, "int%d", i-nbseq2+1);
drapeau=(int*)check_alloc(nbseq, sizeof(int));
drapeau2=(int*)check_alloc(nbseq, sizeof(double));
for(i=0;i<nbseq2;i++) drapeau2[i]=0;
orderedseq=check_alloc(MAXNSP, sizeof(char*));
for(i=0;i<nbseq2;i++){
for(j=0;j<nbseq;j++){
if(!drapeau[j] && strncmp(s_tree->node[i]->nom, seqname[j], MAXLNAME)==0){
drapeau[j]=drapeau2[i]=1;
orderedseq[i]=seq[j];
break;
}
}
if(drapeau2[i]==0){
printf("Taxon %s not found in sequence file.\n", s_tree->node[i]->nom);
exit(EXIT_FAILURE);
}
}
s_tree->nbseq=nbseq=nbseq2;
/* SET "PATTERNS" (relationships between sites) */
s_tree->sitetopatt=check_alloc(lgseq, sizeof(int));
weight=(double*)check_alloc(lgseq, sizeof(double));
for(i=0;i<lgseq;i++) weight[i]=0.;
site=(char*)check_alloc(nbseq, sizeof(char));
lgsite=0;
for(i=0;i<lgseq;i++){
cont=0;
for(j=0;j<nbseq;j++) site[j]=orderedseq[j][i];
for(k=0;k<lgsite;k++){
if(samesite(site, s_tree, k)){
weight[k]++;
cont=1;
break;
}
}
if(cont){
s_tree->sitetopatt[i]=k;
continue;
}
for(j=0;j<nbseq;j++)
s_tree->node[j]->seq[lgsite]=site[j];
weight[lgsite]=1.;
s_tree->sitetopatt[i]=lgsite;
lgsite++;
}
free(drapeau); free(drapeau2); free(site);
s_tree->lgseq=lgsite;
s_tree->weight=weight;
s_tree->weightsum=lgseq;
/* printf("%d species, %d sites, %d patterns\n", nbseq, lgseq, lgsite);*/
/* AMMEND INPUT */
/* ts/tv */
rem_titv=opt->init->INIT_TITV;
if(opt->init->INIT_TITV<=0.){
freq=(double*)check_alloc(16, sizeof(double));
opt->init->INIT_TITV=0.;
nbvrai=nbseq*(nbseq-1)/2;
for(i=0;i<nbseq;i++){
for(j=i+1;j<nbseq;j++){
prov=alsurbet_kim(seq[i], seq[j], freq);
if(prov<-0.5) nbvrai--; else opt->init->INIT_TITV+=prov;
}
}
free(freq);
opt->init->INIT_TITV/=nbvrai;
}
/* root */
rem_root=opt->init->INIT_ROOT;
if(opt->init->INIT_ROOT<=0.){
opt->init->INIT_ROOT=root->l1/(root->l1+root->l2);
if(!bl) opt->init->INIT_ROOT=0.5;
}
/* branch lengths */
s_tree->dist=(double**)check_alloc(nbseq, sizeof(double*));
for(i=0;i<nbseq;i++)
s_tree->dist[i]=(double*)check_alloc(nbseq, sizeof(double));
if(strcmp(opt->init->INIT_LENGTH, "REDO")==0){
for(i=0;i<nbseq;i++){
for(j=i;j<nbseq;j++){
if(i==j) s_tree->dist[i][j]=0.;
else s_tree->dist[i][j]=s_tree->dist[j][i]=gg95(seq[i], seq[j], opt->init->INIT_TITV);
}
}
}
/* ROOT TREE AND ORGANIZE */
organize_tree(NULL, root);
organize_listbr(s_tree);
setpattern(s_tree);
for(ii=0;ii<2*nbseq-3;ii++)
setunderlyingbr(root, s_tree->listbr[ii], ii);
setunderlyinggc(root, s_tree->nbseq);
set_numerobr(root, s_tree->listbr, 2*nbseq-3);
for(i=0;i<nbseq;i++){
s_tree->node[i]->alive1=0;
s_tree->node[i]->alive2=0;
s_tree->node[i]->alive3=1;
}
for(i=nbseq;i<2*nbseq-2;i++){
s_tree->node[i]->alive1=1;
s_tree->node[i]->alive2=1;
s_tree->node[i]->alive3=1;
}
root->alive1=root->alive2=1; root->alive3=-1;
for(ii=0;ii<2*nbseq-3;ii++) s_tree->alivebr[ii]=1;
/* CALL COMPUTE */
if(opt->init->NBRANDOM>0)
nbcompute=opt->init->NBRANDOM;
else
nbcompute=1;
for(l=0;l<nbcompute;l++){
lkh=compute(s_tree, opt->init, opt->compute, opt->converge, opt->print);
if(lkh>maxlkh) maxlkh=lkh;
if(!opt->print->PRINT1 && !opt->print->PRINT2) printf("%f\n", lkh);
}
if(ctree1)
stoc(s_tree->node, nbseq, 1, ctree1, 0);
if(ctree2)
stoc(s_tree->node, nbseq, 1, ctree2, 1);
if(opt->print->EVAL_OUT){
outfile=fopen("detailed_out", "a");
nbtree++;
fprintf(outfile, "%d\t%s\t%f\t%f\t%f\t%f\t%f\t%f\n", nbtree, ctree1, maxlkh, s_tree->titv, s_tree->GCanc, s_tree->gamma_shp, s_tree->covar, s_tree->pi);
fclose(outfile);
}
opt->init->INIT_TITV=rem_titv;
opt->init->INIT_ROOT=rem_root;
/* FREE */
free_tree(s_tree, gamma_nbcl);
free(s_tree);
free_node(root, lgseq, nbparam, 0, gamma_nbcl);
free(orderedseq);
return maxlkh;
}
double maxlike(int nbseq, char** seq, char** seqname, int** ttree, double* lgbi, double* lgbp, int nbbi, int l1, char** list1, int l2, char** list2, options opt, char* ctree, char* ctree1, char* ctree2){
int i, j, k, l, ii, lgseq, lgsite, *drapeau, *drapeau2, cont=0, nbparam, nbvrai;
char **orderedseq, racine, *site;
double *weight, lkh, maxlkh=-1.e100, prov, **lgbi_pt, *freq;
gamma_nbcl=opt->init->GAMMA_NCL;
/* INITIALIZATION */
s_tree=(tree*)check_alloc(1, sizeof(tree));
lgseq=(int)strlen(seq[0]);
s_tree->alivebr=(int*)check_alloc(2*nbseq, sizeof(int));
if(lgbi)
lgbi_pt=(double**)check_alloc(nbseq-2, sizeof(double*));
else
lgbi_pt=NULL;
weight=(double*)check_alloc(lgseq, sizeof(double));
/*
debug_printree(ttree, nbseq, nbbi);
*/
s_tree->node=ttos_unres_rooted(ttree, nbseq, nbbi, seqname, lgbi, lgbp, 0.5, l1, list1, l2, list2, lgbi_pt);
s_tree->nbseq=nbseq;
s_tree->seq=seq;
s_tree->names=seqname;
s_tree->listgc=(double*)check_alloc(2*nbseq, sizeof(double));
s_tree->listbr=(branche*)check_alloc(2*nbseq, sizeof(branche));
s_tree->lgbr_init=(double*)check_alloc(2*nbseq-3, sizeof(double));
for(i=0;i<2*nbseq-2;i++){
s_tree->listbr[i]=(struct branche*)check_alloc(1, sizeof(struct branche));
}
makelistbr_unrooted(NULL, s_tree->node[0], s_tree->listbr, s_tree->alivebr, 2*nbseq-3);
for(i=0;i<2*nbseq-3;i++) s_tree->lgbr_init[i]=s_tree->listbr[i]->length;
s_tree->nbalivebr=0;
for(i=0;i<2*nbseq-3;i++) s_tree->nbalivebr+=s_tree->alivebr[i];
set_var_param(s_tree, opt->compute);
nbparam=s_tree->nb_var_param;
s_tree->classlike_s=(double**)check_alloc(gamma_nbcl, sizeof(double));
for(i=0;i<gamma_nbcl;i++)
s_tree->classlike_s[i]=(double*)check_alloc(lgseq, sizeof(double));
s_tree->like_s=(double*)check_alloc(lgseq, sizeof(double));
s_tree->likeasrv_s=(double*)check_alloc(lgseq, sizeof(double));
s_tree->dlike_s=(double**)check_alloc(nbparam, sizeof(double*));
s_tree->dlikeasrv_s=(double**)check_alloc(nbparam, sizeof(double*));
for(i=0;i<nbparam;i++){
s_tree->dlike_s[i]=(double*)check_alloc(lgseq, sizeof(double));
s_tree->dlikeasrv_s[i]=(double*)check_alloc(lgseq, sizeof(double));
}
s_tree->d2like_s=(double**)check_alloc(nbparam, sizeof(double*));
s_tree->d2likeasrv_s=(double**)check_alloc(nbparam, sizeof(double*));
for(i=0;i<nbparam;i++){
s_tree->d2like_s[i]=(double*)check_alloc(lgseq, sizeof(double));
s_tree->d2likeasrv_s[i]=(double*)check_alloc(lgseq, sizeof(double));
}
s_tree->classdlike_s=(double***)check_alloc(gamma_nbcl, sizeof(double**));
s_tree->classd2like_s=(double***)check_alloc(gamma_nbcl, sizeof(double**));
for(i=0;i<gamma_nbcl;i++){
s_tree->classdlike_s[i]=(double**)check_alloc(nbparam, sizeof(double*));
s_tree->classd2like_s[i]=(double**)check_alloc(nbparam, sizeof(double*));
for(j=0;j<nbparam;j++){
s_tree->classdlike_s[i][j]=(double*)check_alloc(lgseq, sizeof(double));
s_tree->classd2like_s[i][j]=(double*)check_alloc(lgseq, sizeof(double));
}
}
s_tree->deriv=(double*)check_alloc(nbparam, sizeof(double));
s_tree->deriv2=(double*)check_alloc(nbparam, sizeof(double));
for(i=0;i<2*nbseq-2;i++)
alloc_node(s_tree->node[i], lgseq, nbparam, nbseq, (i<nbseq), 0, gamma_nbcl);
alloc_node(root, lgseq, nbparam, nbseq, 0, 0, gamma_nbcl);
for(i=0;i<nbseq;i++){
for(j=0;j<4;j++){ /* 4 patterns for tip nodes */
for(k=0;k<4;k++){ /* 4 possible states */
for(l=0;l<gamma_nbcl;l++){
if(j==k) s_tree->node[i]->x[l][j][k]=1.;
else s_tree->node[i]->x[l][j][k]=0.;
}
}
}
}
for(i=nbseq;i<2*nbseq-2;i++) sprintf(s_tree->node[i]->nom, "int%d", i-nbseq+1);
drapeau=(int*)check_alloc(nbseq, sizeof(int));
drapeau2=(int*)check_alloc(nbseq, sizeof(double));
orderedseq=(char**)check_alloc(nbseq, sizeof(char*));
for(i=0;i<nbseq;i++) drapeau2[i]=0;
for(i=0;i<nbseq;i++){
for(j=0;j<nbseq;j++){
if(!drapeau[j] && strncmp(s_tree->node[i]->nom, seqname[j], MAXLNAME)==0){
drapeau[j]=drapeau2[i]=1;
orderedseq[i]=seq[j];
break;
}
}
if(drapeau2[i]==0){
printf("Taxon %s not found in sequence file.\n", s_tree->node[i]->nom);
exit(EXIT_FAILURE);
}
}
s_tree->nbseq=nbseq;
for(i=0;i<lgseq;i++) weight[i]=0.;
site=(char*)check_alloc(nbseq+1, sizeof(char));
lgsite=0;
for(i=0;i<lgseq;i++){
cont=0;
for(j=0;j<nbseq;j++) site[j]=orderedseq[j][i];
for(k=0;k<lgsite;k++){
if(samesite(site, s_tree, k)){
weight[k]++;
cont=1;
break;
}
}
if(cont) continue;
for(j=0;j<nbseq;j++)
s_tree->node[j]->seq[lgsite]=site[j];
weight[lgsite]=1.;
lgsite++;
}
s_tree->lgseq=lgsite;
s_tree->weight=weight;
s_tree->weightsum=lgseq;
if(opt->init->INIT_TITV<=0.){
freq=(double*)check_alloc(16, sizeof(double));
opt->init->INIT_TITV=0.;
nbvrai=nbseq*(nbseq-1)/2;
for(i=0;i<nbseq;i++){
for(j=i+1;j<nbseq;j++){
prov=alsurbet_kim(seq[i], seq[j], freq);
if(prov<-0.5) nbvrai--; else opt->init->INIT_TITV+=prov;
}
}
opt->init->INIT_TITV/=nbvrai;
free(freq);
}
if(opt->init->INIT_ROOT<=0.){
if(lgbp[0]>-0.5)
opt->init->INIT_ROOT=root->l1/(root->l1+root->l2);
else
opt->init->INIT_ROOT=0.5;
}
s_tree->dist=(double**)check_alloc(nbseq, sizeof(double*));
for(i=0;i<nbseq;i++)
s_tree->dist[i]=(double*)check_alloc(nbseq, sizeof(double));
if(strcmp(opt->init->INIT_LENGTH, "REDO")==0){
for(i=0;i<nbseq;i++){
for(j=i;j<nbseq;j++){
if(i==j) s_tree->dist[i][j]=0.;
else s_tree->dist[i][j]=s_tree->dist[j][i]=gg95(seq[i], seq[j], opt->init->INIT_TITV);
}
}
}
organize_tree(NULL, root);
organize_listbr(s_tree);
setpattern(s_tree);
for(ii=0;ii<2*nbseq-3;ii++)
setunderlyingbr(root, s_tree->listbr[ii], ii);
setunderlyinggc(root, s_tree->nbseq);
set_numerobr(root, s_tree->listbr, 2*nbseq-3);
lkh=compute(s_tree, opt->init, opt->compute, opt->converge, opt->print);
if(lkh>maxlkh) maxlkh=lkh;
if(opt->print->PRINT0)
printf("ln(L)=%f\n", lkh);
if(ctree)
stoc(s_tree->node, 1, nbseq, ctree, -1);
if(ctree1)
stoc(s_tree->node, 1, nbseq, ctree1, 0);
if(ctree2){
set_node_deduced_comp(root);
stoc(s_tree->node, 1, nbseq, ctree2, 1);
}
if(lgbi){
for(i=0;i<nbseq-3;i++){
lgbi[i]=*(lgbi_pt[i]);
}
}
/* FREEING */
free(drapeau); free(drapeau2); free(site); free(orderedseq);
if(lgbi) free(lgbi_pt);
free_tree(s_tree, gamma_nbcl);
free(s_tree);
free_node(root, lgseq, nbparam, 0, gamma_nbcl);
return maxlkh;
}
