PhyloTree::PhyloTree(string tfile){
try {
m = MothurOut::getInstance();
current = CurrentFile::getInstance();
numNodes = 1;
numSeqs = 0;
tree.push_back(TaxNode("Root"));
tree[0].heirarchyID = "0";
tree[0].level = 0;
maxLevel = 0;
calcTotals = true;
string name, tax;
map<string, string> temp;
util.readTax(tfile, temp, true);
for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end();) {
addSeqToTree(itTemp->first, itTemp->second);
temp.erase(itTemp++);
}
string unknownTax = "unknown;";
//added last taxon until you get desired level
for (int i = 1; i < maxLevel; i++) {
unknownTax += "unknown_unclassfied;";
}
addSeqToTree("unknown", unknownTax);
assignHeirarchyIDs(0);
//create file for summary if needed
setUp(tfile);
}
catch(exception& e) {
m->errorOut(e, "PhyloTree", "PhyloTree");
exit(1);
}
}
PhyloTree::PhyloTree(){
try {
m = MothurOut::getInstance();
numNodes = 1;
numSeqs = 0;
tree.push_back(TaxNode("Root"));
tree[0].heirarchyID = "0";
maxLevel = 0;
calcTotals = true;
addSeqToTree("unknown", "unknown;");
}
catch(exception& e) {
m->errorOut(e, "PhyloTree", "PhyloTree");
exit(1);
}
}
int PhyloSummary::summarize(string userTfile){
try {
map<string, string> temp;
m->readTax(userTfile, temp, true);
for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end();) {
addSeqToTree(itTemp->first, itTemp->second);
temp.erase(itTemp++);
}
return numSeqs;
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "summarize");
exit(1);
}
}
