/* 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);
}
void *readSGI(IMAGE *image, unsigned order, unsigned type)
{
int xsize = image->xsize;
int ysize = image->ysize;
int zsize = image->zsize;
size_t count = xsize*ysize*zsize;
int y,z;
switch (type) {
case MM_USH: {
ush *mem;
mallocAss(mem,ush,count);
for (z=0; z < zsize; z++) {
for (y=0; y < ysize; y++) {
getrow(image,rowbuf,y,z);
memcpy((void*)(mem+y*xsize),(void*)rowbuf,sizeof(short)*xsize);
}
}
return mem;
}
case MM_CHR:
case MM_UNC: {
unc *mem;
mallocAss(mem,unc,count);
for (z=0; z < zsize; z++) {
for (y=0; y < ysize; y++) {
getrow(image,rowbuf,y,z);
stoc(rowbuf,charbuf,xsize);
memcpy((void*)(mem+y*xsize),(void*)charbuf,sizeof(unc)*xsize);
}
}
return mem;
}
default: die("readSGI: NOIMP for type %d",type); return NULL;
}
}
int run(vector<string> com, int inorout, int num, int max, int **pifd, int fileInOut, int filein, int fileout)
{
if(DEBUG){
cout << "com size: " << com.size() << endl;
cout << starOfCom(com) << endl;
}
if(com[0] == "ls" || com[0] == "grep")
{
com.push_back("--color=auto");
}
int status = 0;
int star = starOfCom(com);
//char * array[] = {stoc(com[0]), NULL};
int issub = fork();
if(issub == 0){
//signal(SIGUSR1, sigusr1_handler);
/*
if(iB == 1)
{
close(1);
close(0);
setpgrp();
}
*/
setpgrp();
if(inorout == PIPE_IN)
{
for(int i = 0; i < max; i++)
{
if(DEBUG)
cout << com[0] << " in!!! max: " << max << " i : " << i << endl;
if(i != num)
{
if(DEBUG)
cout << ">" << com[0] << " close " << i << endl;
close(pifd[i][0]);
close(pifd[i][1]);
}
}
close(pifd[num][0]);
dup2(pifd[num][1], 1);
close(pifd[num][1]);
}
else if(inorout == PIPE_IAO)
{
for(int i = 0; i < max; i++)
{
if(DEBUG)
cout << com[0] << " in!!! max: " << max << " i : " << i << endl;
if(i != num && i != num+1)
{
if(DEBUG)
cout << com[0] << " close " << i << endl;
close(pifd[i][0]);
close(pifd[i][1]);
}
}
close(pifd[num][1]);
dup2(pifd[num][0], 0);
close(pifd[num][0]);
close(pifd[num+1][0]);
dup2(pifd[num+1][1], 1);
close(pifd[num+1][1]);
}
else if(inorout == PIPE_OUT)
{
for(int i = 0; i < max; i++)
{
if(DEBUG)
cout << com[0] << " in!!! max: " << max << " i : " << i << endl;
if(i != num)
{
if(DEBUG)
cout << ">" << com[0] << " close " << i << endl;
close(pifd[i][0]);
close(pifd[i][1]);
}
}
close(pifd[num][1]);
dup2(pifd[num][0], 0);
close(pifd[num][0]);
}
if(fileInOut == F_IN)
dup2(filein, 0);
else if(fileInOut == F_OUT || fileInOut == F_APP)
dup2(fileout, 1);
else if(fileInOut == F_IN_AND_OUT || fileInOut == F_IN_AND_APP)
{
dup2(filein, 0);
dup2(fileout, 1);
}
if(star == 0)
{
char ** arg = (char **)malloc((com.size()+ 1) * sizeof(char *));
for(int i = 0; i < com.size(); i++){
arg[i] = stoc(com[i]);
}
arg[com.size()] = NULL;
execvp(com[0].c_str(), arg);
cout << com[0] << ": command not found" << endl;
for(int i = 0; i <= com.size(); i++)
{
free(arg[i]);
}
free(arg);
exit(-1);
}
else {
glob_t globbuf;
globbuf.gl_offs = com.size() - star;
int comnum = 0;
bool isNumOne = 1;
for(int i = 0; i < com.size(); i++){
if(com[i].find('*') != string::npos){
if(isNumOne){
glob(com[i].c_str(), GLOB_DOOFFS, NULL, &globbuf);
isNumOne = 0;
}
else
glob(com[i].c_str(), GLOB_DOOFFS | GLOB_APPEND,
NULL, &globbuf);
}
}
for(int i = 0; i < com.size(); i++){
if(com[i].find('*') == string::npos){
globbuf.gl_pathv[comnum] = stoc(com[i]);
comnum ++;
}
}
execvp(com[0].c_str(), &globbuf.gl_pathv[0]);
cout << com[0] << ": command not found" << endl;
for(int i = 0; i < globbuf.gl_offs; i++)
{
free(globbuf.gl_pathv[i]);
}
exit(-1);
}
}
else {
if(inorout == PIPE_NONE && iB != 1)
{
needSig = 1;
nowcpid = issub;
waitpid(issub, &status, WUNTRACED);
if(WIFSTOPPED(status))
{
if(DEBUG)
cout << "stop!" << endl;
JOB j;
j.pid = issub;
j.stat = 1;
j.com = jobname;
vecJ.push_back(j);
}
}
if(iB == 1)
{
JOB j;
j.pid = issub;
j.stat = 2;
j.com = jobname;
vecJ.push_back(j);
}
}
if(DEBUG)
cout << "end " << com[0] << endl;
return status;
}
int runpipe(vector<vector<string> > com)
{
bool hasInFile = false;
string inFile = "";
bool hasOutFile = false;
bool hasAppFile = false;
string outFile = "";
iB = 0;
jobname = "";
for(int i = 0; i < com.size(); i++)
{
for(int j = 0; j < com[i].size(); j++)
{
jobname += com[i][j];
jobname += " ";
}
}
if(DEBUG)
cout << jobname << endl;
for (vector<vector<string> >::iterator it = com.begin(); it != com.end();)
{
if ((*it)[0] == "|"){
(*it).erase((*it).begin());
it++;
}
else if((*it)[0] == "<")
{
hasInFile = true;
inFile = (*it).back();
it = com.erase(it);
}
else if((*it)[0] == ">")
{
hasOutFile = true;
hasAppFile = false;
outFile = (*it).back();
it = com.erase(it);
}
else if((*it)[0] == ">>")
{
hasOutFile = false;
hasAppFile = true;
outFile = (*it).back();
it = com.erase(it);
}
else if((*it)[0] == "&")
{
iB = 1;
it = com.erase(it);
}
else {
it++;
}
}
int ifd, ofd;
if(hasInFile == true)
{
if(DEBUG)
cout << "In: " << inFile << endl;
ifd = open(stoc(inFile), O_RDONLY);
}
if(hasAppFile == true)
{
if(DEBUG)
cout << "App: " << outFile << endl;
ofd = open(stoc(outFile), O_APPEND|O_CREAT|O_WRONLY, 0666);
}
if(hasOutFile == true)
{
if(DEBUG)
cout << "Out: " << outFile << endl;
remove(stoc(outFile));
ofd = open(stoc(outFile), O_RDWR|O_CREAT, 0666);
}
if(DEBUG)
cout << "com size: " << com.size() << endl;
int stat;
if (com.size() == 1)
{
if(hasInFile && !hasOutFile && !hasAppFile)
stat = run(com[0], PIPE_NONE, -1, -1, NULL, F_IN, ifd, 0);
else if(!hasInFile && hasOutFile && !hasAppFile)
stat = run(com[0], PIPE_NONE, -1, -1, NULL, F_OUT, 0, ofd);
else if(hasInFile && hasOutFile && !hasAppFile)
stat = run(com[0], PIPE_NONE, -1, -1, NULL, F_IN_AND_OUT, ifd, ofd);
else if(!hasInFile && !hasOutFile && hasAppFile)
stat = run(com[0], PIPE_NONE, -1, -1, NULL, F_APP, 0, ofd);
else if(hasInFile && !hasOutFile && hasAppFile)
stat = run(com[0], PIPE_NONE, -1, -1, NULL, F_IN_AND_APP, ifd, ofd);
else
stat = run(com[0], PIPE_NONE, -1, -1, NULL, F_NONE, 0, 0);
}
else if (com.size() >= 2)
{
int ** pifd = (int**)malloc((com.size()-1) * sizeof(int*));
for(int i = 0; i < com.size() - 1; i++)
{
pifd[i] = (int*)malloc(2 * sizeof(int));
if(pipe(pifd[i]) < 0)
{
cout << i << " pipe error" << endl;
return -1;
}
}
if(DEBUG)
cout << "com.size() : " <<com.size() << endl;
if(hasInFile)
run(com[0], PIPE_IN, 0, com.size() - 1, pifd, F_IN, ifd, 0);
else
run(com[0], PIPE_IN, 0, com.size() - 1, pifd, F_NONE, 0, 0);
for(int i = 1; i < com.size() - 1; i++)
{
run(com[i], PIPE_IAO, i-1, com.size() - 1, pifd, F_NONE, 0, 0);
}
if(hasAppFile)
run(com[com.size()-1], PIPE_OUT, com.size()- 2, com.size() - 1, pifd, F_APP, 0, ofd);
else if(hasOutFile)
run(com[com.size()-1], PIPE_OUT, com.size()- 2, com.size() - 1, pifd, F_OUT, 0, ofd);
else
run(com[com.size()-1], PIPE_OUT, com.size()- 2, com.size() - 1, pifd, F_NONE, 0, 0);
for(int i = 0; i < com.size() - 1; i++)
{
close(pifd[i][0]);
close(pifd[i][1]);
}
do
{
if(DEBUG)
cout << "wait" << endl;
}
while(wait(&stat) != -1);
if(hasInFile)
close(ifd);
if(hasOutFile || hasAppFile)
close(ofd);
for(int i = 0; i < com.size() - 1; i++)
free(pifd[i]);
free(pifd);
}
return stat;
}
//MString unitostr(const short *s, const int sz);
MStringS::operator MString(){ return stoc((unsigned short*)data, sz); }
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;
}
