/* BEGIN DEFUNCT */
obreak()
{
struct a {
char *nsiz;
};
register size_t n, d, ds;
/*
* set n to new data size
*/
n = btoc(((struct a *)u.u_ap)->nsiz) - ctos(u.u_tsize) * stoc(1);
if (n < 0)
n = 0;
/*
* since we can't pass a -ve argument for the difference to chksize,
* if d is negative, make ds equal to the final value and clear d.
* keep the real difference in n for later use in expand.
*/
ds = u.u_dsize;
if ((n = d = clrnd(n - u.u_dsize)) < 0) {
ds += d;
d = 0;
}
if (ctob(ds + d) > u.u_rlimit[RLIMIT_DATA].rlim_cur) {
u.u_error = ENOMEM;
return;
}
if (chksize((u_int)u.u_tsize, (u_int)ds, (u_int)d, (u_int)u.u_ssize))
return;
if (swpexpand(ds + d, u.u_ssize, &u.u_dmap, &u.u_smap) == 0)
return;
expand((int)n, 0);
}
MStringS::MStringS(const char* string){ if(!string){ data=0; sz=0; return ; }
int size=strlen(string);
if (!size) {data=0; return ;}
data=(short*)new char[size*2+2];
//MString ret; ret.Reserv(size);
for(int i=0; i<size; i++) data[i]=ctos(string[i]);
sz=size; data[sz]=0;
}
void squareImageLabel::removeHashSquare(const pixel& p) {
// (pixels identify on coordinates, not colors)
if (hashSquares_.removeOne(p)) {
hashSquaresToBeRemoved_.push_back(p);
--lastHashDrawn_;
}
else {
qWarning() << "Pixel not found on remove" << hashSquares_.size() <<
p.x() << p.y() << ctos(p.color());
}
}
/* Affichage des constantes d'un L-System donne */
String dispConstants(String constants)
{
int i=0;
String strLsystem = (String)malloc(50*sizeof(char));
strcpy (strLsystem,"");
strcat(strLsystem,"Constants: {");
for(i=0;i<(int)strlen(constants);i++){
strcat(strLsystem,ctos(constants[i]));
if (i!=(int)strlen(constants)-1) strcat(strLsystem,",");
}
strcat(strLsystem,"}\n");
return strLsystem;
}
/* Affichage des variables de l'alphabet d'un L-System donne */
String dispVariables(String variables)
{
int i = 0;
String strLsystem = (String)malloc(50*sizeof(char));
strcpy (strLsystem,"");
strcat(strLsystem,"Variables: {");
for(i=0;i<(int)strlen(variables);i++){
strcat(strLsystem,ctos(variables[i]));
if (i!=(int)strlen(variables)-1) strcat(strLsystem,",");
}
strcat(strLsystem,"}\n");
return strLsystem;
}
/* Affichage des regles correspondantes a chacune des variables d'un L-System donne */
String dispRules (Rules* teteliste, String variables)
{
String str = (String)malloc(200*sizeof(char));
strcpy (str,"");
Rules* l = teteliste;
double i=0;
while (l!=NULL)
{
str = strcat(str,"( ");
str = strcat(str,ctos(variables[(int)i]));
str = strcat(str," -> ");
str = strcat(str,l->rule);
str = strcat(str," ) ");
i = i+1;
l = l->next;
}
return str;
}
/* Renvoi de la generation suivante d'une generation donnee pour un L-System donne */
String nextGen(String generation, Lsystem lsystem)
{
String generation2=(String)malloc((double)strlen(generation)*sizeof(char));
strcpy (generation2,"");
double i = 0;
double lenghtTot = (double)strlen(generation);
while (i<(double)strlen(generation)){
int nbVar = isVariable(generation[(int)i],lsystem);
if (nbVar==-1) strcat(generation2,ctos(generation[(int)i]));
else {
int j;
Rules* l = lsystem.rules;
for (j=0;j<nbVar;j++){
l = l->next;
}
lenghtTot = lenghtTot+(double)strlen(l->rule);
generation2 = (String)realloc(generation2,lenghtTot*sizeof(char));
strcat(generation2,l->rule);
}
i = i+1;
}
return generation2;
}
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;
}