tree[0].heirarchyID = "0";
maxLevel = 0;
calcTotals = true;
+ addSeqToTree("unknown", "unknown;");
}
catch(exception& e) {
m->errorOut(e, "PhyloTree", "PhyloTree");
maxLevel = 0;
calcTotals = true;
string name, tax;
-
#ifdef USE_MPI
int pid, num, processors;
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- ifstream in;
- m->openInputFile(tfile, in);
-
- //read in users taxonomy file and add sequences to tree
- while(!in.eof()){
- in >> name >> tax; m->gobble(in);
-
- addSeqToTree(name, tax);
- }
- in.close();
+ map<string, string> temp;
+ m->readTax(tfile, temp);
+
+ for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end();) {
+ addSeqToTree(itTemp->first, itTemp->second);
+ temp.erase(itTemp++);
+ }
#endif
assignHeirarchyIDs(0);
-
+
+
+ string unknownTax = "unknown;";
+ //added last taxon until you get desired level
+ for (int i = 1; i < maxLevel; i++) {
+ unknownTax += "unclassfied;";
+ }
+
+ addSeqToTree("unknown", unknownTax);
+
//create file for summary if needed
setUp(tfile);
}
int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
try {
-
numSeqs++;
map<string, int>::iterator childPointer;
int level = 1;
tree[0].accessions.push_back(seqName);
+ m->removeConfidences(seqTaxonomy);
+
string taxon;// = getNextTaxon(seqTaxonomy);
while(seqTaxonomy != ""){
map<string, int>::iterator childPointer;
vector<TaxNode> copy = tree;
-
+
//fill out tree
fillOutTree(0, copy);
void PhyloTree::print(ofstream& out, vector<TaxNode>& copy){
try {
-
+
//output mothur version
out << "#" << m->getVersion() << endl;
out << copy.size() << endl;
out << maxLevel << endl;
-
+
for (int i = 0; i < copy.size(); i++) {
-
+
out << copy[i].level << '\t'<< copy[i].name << '\t' << copy[i].children.size() << '\t';
map<string,int>::iterator it;
try {
bool okay = true;
+ templateFileNames.push_back("unknown");
map<string, int>::iterator itFind;
map<string, int> taxonomyFileNames = name2Taxonomy;
+ if (m->debug) { m->mothurOut("[DEBUG]: in error check. Numseqs in template = " + toString(templateFileNames.size()) + ". Numseqs in taxonomy = " + toString(taxonomyFileNames.size()) + ".\n"); }
+
for (int i = 0; i < templateFileNames.size(); i++) {
itFind = taxonomyFileNames.find(templateFileNames[i]);
if (itFind != taxonomyFileNames.end()) { //found it so erase it
taxonomyFileNames.erase(itFind);
}else {
- m->mothurOut(templateFileNames[i] + " is in your template file and is not in your taxonomy file. Please correct."); m->mothurOutEndLine();
+ m->mothurOut("'" +templateFileNames[i] + "' is in your template file and is not in your taxonomy file. Please correct."); m->mothurOutEndLine();
okay = false;
}
- templateFileNames.erase(templateFileNames.begin()+i);
- i--;
+ //templateFileNames.erase(templateFileNames.begin()+i);
+ //i--;
}
+ templateFileNames.clear();
if (taxonomyFileNames.size() > 0) { //there are names in tax file that are not in template
okay = false;