changes while testing

[mothur.git] / phylotree.cpp

diff --git a/phylotree.cpp b/phylotree.cpp
index 8a7c712b0f255db20da492fd95bc15d3116ce151..b9bab4ec2934a4121305f87111cf2d238f5ec4d5 100644 (file)
--- a/phylotree.cpp
+++ b/phylotree.cpp
@@ -259,6 +259,8 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
                        //somehow the parent is getting one too many accnos
                        //use print to reassign the taxa id
                        taxon = getNextTaxon(seqTaxonomy, seqName);
+            
+            if (m->debug) { m->mothurOut(seqName +'\t' + taxon +'\n'); }
                        
                        if (taxon == "") {  m->mothurOut(seqName + " has an error in the taxonomy.  This may be due to a ;;"); m->mothurOutEndLine(); if (currentNode != 0) {  uniqueTaxonomies.insert(currentNode); } break;  }
                        
@@ -341,6 +343,9 @@ void PhyloTree::assignHeirarchyIDs(int index){
                int counter = 1;
                
                for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
+            
+            if (m->debug) { m->mothurOut(toString(index) +'\t' + tree[it->second].name +'\n'); }
+                
                        tree[it->second].heirarchyID = tree[index].heirarchyID + '.' + toString(counter);
                        counter++;
                        tree[it->second].level = tree[index].level + 1;
@@ -399,6 +404,8 @@ void PhyloTree::binUnclassified(string file){
                        }
                }
                
+        if (m->debug) { m->mothurOut("maxLevel = " + toString(maxLevel) +'\n'); }
+        
                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
@@ -409,11 +416,14 @@ void PhyloTree::binUnclassified(string file){
                        
                        int level = copy[itLeaf->second].level;
                        int currentNode = itLeaf->second;
+            
+            if (m->debug) { m->mothurOut(copy[currentNode].name +'\n'); }
                        
                        //this sequence is unclassified at some levels
                        while(level < maxLevel){
                
                                level++;
+                if (m->debug) { m->mothurOut("level = " + toString(level) +'\n'); }
                        
                                string taxon = "unclassified";