void tree2dataS(FILE * tree,int n,int m,int* &P,double* &B,string* &Support,string* &leaves){
int inode = 0;//number of internal nodes;
stack<int> pileNode;
char c = readBracket(tree,"input tree");
int a=1;
int countleaf=n;
P[0]=-1;
B[0]=-1;
do{
c = readChar(tree,"input tree");
if (c==')'){
a--;inode++;
int s1=pileNode.top();pileNode.pop();
int s2=pileNode.top();pileNode.pop();
P[s1]=n-inode;
P[s2]=n-inode;
if (a>0){
Support[n-inode]=readSupport(tree,"input tree");
B[n-inode]=readdouble(tree,"input tree");
}
else while (!pileNode.empty()){
int s=pileNode.top();pileNode.pop();
P[s]=n-inode;
}
pileNode.push(n-inode);
}
else if (c!='(' && c!=',' && c!=-1 && c!=';' && c!='\n'){
string lb=readLabel(c,tree);
pileNode.push(countleaf);
leaves[countleaf]=lb;
B[countleaf]=readdouble(tree,"input tree");
Support[countleaf]="";
countleaf++;
}
else if (c=='(') {a++;}
} while (a>0);
}
void counting(string fn,int &n,int &m,int nb_tree){
FILE * tree = fopen(fn.c_str(),"rt");
if (tree==NULL) cout<<"Impossible to open tree file"<<endl;
else{
int n1,m1;
for (int i=0;i<nb_tree;i++){
char c = readBracket(tree,fn);
n=0;//internal nodes
int l=0;//leaves
int a=0;
while (c!=';'){
if (c=='(') {n++;a++;}
if (c==':' && a>0) l++;
if (c==')') {
a--;
if (a>0) read2P(tree,fn);
}
c=readChar(tree,fn);
}
if (a!=0) {
cout<<"Errors in the input trees"<<endl;
exit(EXIT_FAILURE);
}
m=n+l-1;//number of branches
if (i>0 && n1!=n && m1!=m){
cout<<"The trees do not have the same size"<<endl;
exit (EXIT_FAILURE);
}
if (i==0){
n1=n;
m1=m;
}
}
fclose(tree);
}
}
bool tree2data(FILE * tree,string date,int n,int m,int* &P,double* &B,string* &Support,double* &T,string* &leaves){
int inode = 0;//number of internal nodes;
stack<int> pileNode;
char c = readBracket(tree,"input tree");
int a=1;
int countleaf=n;
P[0]=-1;
B[0]=-1;
bool all=false;
do{
c = readChar(tree,"input tree");
if (c==')'){
a--;inode++;
int s1=pileNode.top();pileNode.pop();
int s2=pileNode.top();pileNode.pop();
P[s1]=n-inode;
P[s2]=n-inode;
if (a>0){
Support[n-inode]=readSupport(tree,"input tree");
B[n-inode]=readdouble(tree,"input tree");
}
else
while (!pileNode.empty()){
int s=pileNode.top();pileNode.pop();
P[s]=n-inode;
}
pileNode.push(n-inode);
}
else if (c!='(' && c!=',' && c!=-1 && c!=';' && c!='\n'){
string lb=readLabel(c,tree);
pileNode.push(countleaf);
leaves[countleaf]=lb;
B[countleaf]=readdouble(tree,"input tree");
Support[countleaf]="";
countleaf++;
}
else if (c=='(') {a++;}
} while (a>0);
FILE * dateFile = fopen(date.c_str(),"rt");
if (dateFile == NULL) cout << "Can not open the file " <<date<< endl;
else{
int ino=readInt(dateFile,"Error in the date file, the file should begin with an integer (the number of dated tips)");
for (int i=0;i<=m;i++) T[i]=-1;
int count=0;
double first=-1;
for (int i=0;i<ino;i++){
string s=readWord(dateFile,date);
double lt=readdouble(dateFile,date);
int k = getPosition(leaves,s,n,m+1);
if (k!=-1) {
if (count==0) first=lt;
else if (lt!=first) all=true;
T[k]=lt;
count++;
}
}
if (count<countleaf-n){
cout<<"The dates of some taxa are missing. If the input tree contains some outgroups, use option -g to specify the file name of outgroups. "<<endl;
exit(EXIT_FAILURE);
}
fclose(dateFile);
}
return all;
}
void checkRooted(Pr* opt){
FILE * tree = fopen(opt->inFile.c_str(),"rt");
if (tree==NULL){
cout<<"Error: can not open the input file"<<endl;
exit(EXIT_FAILURE);
}
stack<int> pileNode;
char c = readBracket(tree,"input tree");
int a=1;
int s=0;
int nbChild=0;
int n=0;
int m=0;
do{
c = readChar(tree,"input tree");
if (c==')'){
a--;
s=0;
nbChild=0;
while (!pileNode.empty() && s!=-1) {
s=pileNode.top();pileNode.pop();
if (s!=-1){
nbChild++;
}
}
string sp=readSupport(tree,"input tree");
if (a>0) {
double d = readdouble(tree,"input tree");
}
pileNode.push(1);
n++;
m++;
}
else if (c!='(' && c!=',' && c!=-1 && c!=';' && c!='\n'){
string s= readLabel(c,tree,a);
pileNode.push(1);
double d =readdouble(tree,"input tree");
m++;
}
else if (c=='(') {a++;pileNode.push(-1);}
else if (c=='\n') {
c=readChar(tree,"input tree");
}
} while (a>0);
fclose(tree);
m--;
opt->nbINodes=n;
opt->nbBranches=m;
if (m==2*n) {
opt->rooted=true;
}
else if (m==2*n+1 && nbChild==3){
opt->rooted=false;
}
else if (nbChild==2) {
opt->rooted=true;
}
else{
opt->rooted=false;
}
}