changes for 1.12.2

[mothur.git] / phylotree.cpp

diff --git a/phylotree.cpp b/phylotree.cpp
index d085f6c52ce3c733c7666d1c7df28e95a0575647..6b32e27201b5103e077261117f21fe30b69eb31c 100644 (file)
--- a/phylotree.cpp
+++ b/phylotree.cpp
@@ -370,18 +370,18 @@ void PhyloTree::binUnclassified(string file){
                map<string, int>::iterator childPointer;
                
                vector<TaxNode> copy = tree;
-                               
+                       
                //fill out tree
                fillOutTree(0, copy);
-               
-               //get leaf nodes that may need externsion
+       
+               //get leaf nodes that may need extension
                for (int i = 0; i < copy.size(); i++) {  
 
                        if (copy[i].children.size() == 0) {
                                leafNodes[i] = i;
                        }
                }
-               
+       //cout << "maxLevel = " << maxLevel << endl;    
                int copyNodes = copy.size();
                
                //go through the seqs and if a sequence finest taxon is not the same level as the most finely defined taxon then classify it as unclassified where necessary
@@ -394,7 +394,7 @@ void PhyloTree::binUnclassified(string file){
                        int currentNode = itLeaf->second;
                        
                        //this sequence is unclassified at some levels
-                       while(level <= maxLevel){
+                       while(level < maxLevel){
                
                                level++;
                        
@@ -434,19 +434,21 @@ void PhyloTree::fillOutTree(int index, vector<TaxNode>& copy) {
        try {
                map<string,int>::iterator it;
                
-               it = copy[index].children.find("unclassified");
-               if (it == copy[index].children.end()) { //no unclassified at this level
-                       string taxon = "unclassified";
-                       copy.push_back(TaxNode(taxon));
-                       copy[index].children[taxon] = copy.size()-1;
-                       copy[copy.size()-1].parent = index;
-                       copy[copy.size()-1].level = copy[index].level + 1;
-               }
+               if (copy[index].level < maxLevel) {
+                       it = copy[index].children.find("unclassified");
+                       if (it == copy[index].children.end()) { //no unclassified at this level
+                               string taxon = "unclassified";
+                               copy.push_back(TaxNode(taxon));
+                               copy[index].children[taxon] = copy.size()-1;
+                               copy[copy.size()-1].parent = index;
+                               copy[copy.size()-1].level = copy[index].level + 1;
+                       }
                
-               if (tree[index].level <= maxLevel) {
-                       for(it=tree[index].children.begin();it!=tree[index].children.end();it++){ //check your children
+                       
+                       for(it=copy[index].children.begin();it!=copy[index].children.end();it++){ //check your children
                                fillOutTree(it->second, copy);
                        }
+                       
                }
                
        }