int ReadTree::readSpecialChar(istream& f, char c, string name) {
try {
- gobble(f);
+ m->gobble(f);
char d = f.get();
if(d == EOF){
exit(1);
}
if(d == ')' && f.peek() == '\n'){
- gobble(f);
+ m->gobble(f);
}
return d;
}
int ReadTree::readNodeChar(istream& f) {
try {
// while(isspace(d=f.get())) {;}
- gobble(f);
+ m->gobble(f);
char d = f.get();
if(d == EOF){
m->mothurOut("Error: Missing branch length in input tree.\n");
exit(1);
}
- gobble(f);
+ m->gobble(f);
return b;
}
catch(exception& e) {
//save trees for later commands
globaldata->gTree.push_back(T);
- gobble(filehandle);
+ m->gobble(filehandle);
}
//if you are a nexus file
}else if ((c = filehandle.peek()) == '#') {
if(f.peek() == ':'){
readSpecialChar(f,':',"colon");
- if(n >= numNodes){ m->mothurOut("Error: Too many nodes in input tree\n"); readOk = -1; return -1; }
+ if(n >= numNodes){ m->mothurOut("Error: Too many nodes in input tree\n"); readOk = -1; return -1; }
T->tree[n].setBranchLength(readBranchLength(f));
}else{