void CNPLCM_CR_Basic_Freq::permute_latent_classes_by_nu(){
//reorder latent classes increasingly according to nuK.
std::vector<int> new2old(par->K), old2new(par->K);
std::vector<_CNPLCM_CR_Basic_Freq_mypair> s_index(par->K);
for (int k = 0; k < par->K; k++){
s_index[k].first = 1.0 - par->nuK[k];
s_index[k].second = k;
}
std::sort(s_index.begin(), s_index.end(), _CNPLCM_CR_Basic_Freq_comparator);
std::vector<int> perm(K);
for (int k = 0; k < par->K; k++){
new2old[k] = s_index[k].second;
} // new2old[a] == b <=> former b-th element is now a-th element.
for (int k = 0; k < par->K; k++){
old2new[ new2old[k] ] = k;
}
CParams_NPLCM_CR_Basic_Freq *tmp = new CParams_NPLCM_CR_Basic_Freq(*par);
//for (int i = 0; i < par->n; i++){
// tmp->zI[i] = old2new[ par->zI[i] ];
//}
for (int m = 0; m < par->M; m++){
for (int k = 0; k < par->K; k++){
tmp->count_zIK[m][k] = par->count_zIK[m][ new2old[k] ];
}
}
for (int j = 0; j < par->J; j++){
for (int k = 0; k < par->K; k++){
tmp->lambdaJK[j][k] = par->lambdaJK[j][ new2old[k] ];
tmp->aux_JK2[j][k][0] = par->aux_JK2[j][ new2old[k] ][0];
tmp->aux_JK2[j][k][1] = par->aux_JK2[j][ new2old[k] ][1];
}
}
for (int k = 0; k < par->K; k++){
tmp->nuK[k] = par->nuK[new2old[k]];
tmp->log_nuK[k] = par->log_nuK[new2old[k]];
tmp->countK[k] = par->countK[new2old[k]];
tmp->count0K[k] = par->count0K[new2old[k]];
}
//std::copy(tmp->zI, tmp->zI + par->n, par->zI);
std::copy(tmp->count_zIK[0], tmp->count_zIK[0] + par->M * par->J, par->count_zIK[0]);
std::copy(tmp->lambdaJK[0], tmp->lambdaJK[0] + par->J * par->K, par->lambdaJK[0]);
std::copy(tmp->aux_JK2[0][0], tmp->aux_JK2[0][0] + par->J * par->K * 2, par->aux_JK2[0][0]);
std::copy(tmp->nuK, tmp->nuK + par->K, par->nuK);
std::copy(tmp->log_nuK, tmp->log_nuK + par->K, par->log_nuK);
std::copy(tmp->countK, tmp->countK + par->K, par->countK);
std::copy(tmp->count0K, tmp->count0K + par->K, par->count0K);
delete tmp;
}
void Tree::reorderSeqs (vguard<FastSeq>& seq) const {
Assert (seq.size() == nodes(), "Number of sequences doesn't match number of nodes in tree");
map<string,size_t> name2seq;
for (size_t n = 0; n < seq.size(); ++n) {
Assert (name2seq.find (seq[n].name) == name2seq.end(), "Duplicate sequence name: %s", seq[n].name.c_str());
name2seq[seq[n].name] = n;
}
vguard<size_t> new2old (seq.size()), old2new (seq.size());
for (TreeNodeIndex n = 0; n < nodes(); ++n) {
Assert (name2seq.find (seqName(n)) != name2seq.end(), "Tree node %s is absent from sequence dataset", seqName(n).c_str());
const size_t old_n = name2seq[seqName(n)];
new2old[n] = old_n;
old2new[old_n] = n;
}
for (size_t n = 0; n < new2old.size(); ++n) {
const size_t o = new2old[n], m = old2new[n];
swap (seq[n], seq[o]);
swap (old2new[n], old2new[o]);
swap (new2old[n], new2old[m]);
}
}
struct utmpx *
pututxline(const struct utmpx *utx)
{
struct utmpx temp, *u = NULL;
int gotlock = 0;
_DIAGASSERT(utx != NULL);
if (utx == NULL)
return NULL;
if (strcmp(_PATH_UTMPX, utfile) == 0) {
if (geteuid() == 0) {
if (fp != NULL && readonly)
endutxent();
} else {
if (fp == NULL || readonly)
return utmp_update(utx);
}
}
(void)memcpy(&temp, utx, sizeof(temp));
if (fp == NULL) {
(void)getutxent();
if (fp == NULL || readonly)
return NULL;
}
if (getutxid(&temp) == NULL) {
setutxent();
if (getutxid(&temp) == NULL) {
if (lockf(fileno(fp), F_LOCK, (off_t)0) == -1)
return NULL;
gotlock++;
if (fseeko(fp, (off_t)0, SEEK_END) == -1)
goto fail;
}
}
if (!gotlock) {
/* we are not appending */
if (fseeko(fp, -(off_t)sizeof(ut), SEEK_CUR) == -1)
return NULL;
}
if (version == 1)
new2old(&temp);
if (fwrite(&temp, sizeof (temp), 1, fp) != 1)
goto fail;
if (fflush(fp) == -1)
goto fail;
u = memcpy(&ut, &temp, sizeof(ut));
fail:
if (gotlock) {
if (lockf(fileno(fp), F_ULOCK, (off_t)0) == -1)
return NULL;
}
return u;
}
