fixed bug with shhh.flow from file path name in write functions, added "smart" featur...

[mothur.git] / phylotree.cpp

diff --git a/phylotree.cpp b/phylotree.cpp
index e430fb9e85622dcd1d425534857fe37dff600da9..dba1e3b56951f8ae1c484ace22187a9b65053d35 100644 (file)
--- a/phylotree.cpp
+++ b/phylotree.cpp
@@ -20,6 +20,7 @@ PhyloTree::PhyloTree(){
                tree[0].heirarchyID = "0";
                maxLevel = 0;
                calcTotals = true;
+               addSeqToTree("unknown", "unknown;");
        }
        catch(exception& e) {
                m->errorOut(e, "PhyloTree", "PhyloTree");
@@ -127,6 +128,7 @@ PhyloTree::PhyloTree(string tfile){
                maxLevel = 0;
                calcTotals = true;
                string name, tax;
+               addSeqToTree("unknown", "unknown;");
 
                
                #ifdef USE_MPI
@@ -232,7 +234,6 @@ string PhyloTree::getNextTaxon(string& heirarchy, string seqname){
 
 int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
        try {
-                       
                numSeqs++;
                
                map<string, int>::iterator childPointer;
@@ -375,7 +376,7 @@ void PhyloTree::binUnclassified(string file){
                map<string, int>::iterator childPointer;
                
                vector<TaxNode> copy = tree;
-                       
+               
                //fill out tree
                fillOutTree(0, copy);
        
@@ -484,16 +485,16 @@ string PhyloTree::getFullTaxonomy(string seqName) {
 
 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;
@@ -606,6 +607,7 @@ bool PhyloTree::ErrorCheck(vector<string> templateFileNames){
        try {
        
                bool okay = true;
+               templateFileNames.push_back("unknown");
                
                map<string, int>::iterator itFind;
                map<string, int> taxonomyFileNames = name2Taxonomy;