void toNormalizedNEXUS(ifstream & inf, ostream *os)
{
NxsTaxaBlock taxa;
NxsTreesBlock trees(&taxa);
NxsAssumptionsBlock assumptions(&taxa);
NxsCharactersBlock character(&taxa, &assumptions);
NxsDataBlock data(&taxa, &assumptions);
NxsDistancesBlock distances(&taxa);
NxsUnalignedBlock unaligned(&taxa, &assumptions);
NormalizingReader nexus(os);
nexus.Add(&taxa);
nexus.Add(&trees);
nexus.Add(&assumptions);
nexus.Add(&character);
nexus.Add(&data);
nexus.Add(&distances);
nexus.Add(&unaligned);
if (os)
{
*os << "#NEXUS\n";
}
NormalizingToken token(inf, os);
nexus.Execute(token);
}
int main(int argc, char const *argv[]){
pthread_mutex_init(&lock, NULL);
pthread_create(&thread_id, NULL, checkIDLE, (void*)NULL);
if(argc==4) nexus(argv);
else {printf("Format: %s <username> <server> <port>\n", argv[0]); exit(EXIT_FAILURE);}
pthread_mutex_destroy(&lock);
pthread_join(thread_id, NULL);
return 0;
}
int main(int , char *argv[])
{
taxa = new NxsTaxaBlock();
trees = new NxsTreesBlock(taxa);
MyReader nexus(argv[1], argv[2]);
nexus.Add(taxa);
nexus.Add(trees);
MyToken token(nexus.inf, nexus.outf);
nexus.Execute(token);
taxa->Report(nexus.outf);
trees->Report(nexus.outf);
return 0;
}
string nexus(int i,Pr* pr,Node** nodes){
ostringstream b,date;
if (i>0){
b<<nodes[i]->B;
}
date<<nodes[i]->D;
if (i>=pr->nbINodes) return nodes[i]->L+"[&date="+date.str()+"]:"+b.str();
else{
string newLabel="(";
for (vector<int>::iterator iter=nodes[i]->suc.begin(); iter!=nodes[i]->suc.end(); iter++) {
int s = *iter;
string l=nexus(s,pr,nodes);
if (iter==nodes[i]->suc.begin()) newLabel+=l;
else newLabel+=","+l;
}
if (i>0) {
if (myabs(nodes[i]->B)>toCollapse) return newLabel+")"+nodes[i]->L+"[&date="+date.str()+"]:"+b.str();
else return newLabel+")"+nodes[i]->L+":"+b.str();
}
else{
return newLabel+")"+nodes[i]->L+"[&date="+date.str()+"];\n";
}
}
}