finished get.relabund command

[mothur.git] / phylotree.cpp

diff --git a/phylotree.cpp b/phylotree.cpp
index 53492cafe6f17fbc2b167c8393dda6c24c72ea55..d6c740ae791b494ea64951a03405b38535593152 100644 (file)
--- a/phylotree.cpp
+++ b/phylotree.cpp
@@ -197,14 +197,22 @@ PhyloTree::PhyloTree(string tfile){
 
 /**************************************************************************************************/
 
-string PhyloTree::getNextTaxon(string& heirarchy){
+string PhyloTree::getNextTaxon(string& heirarchy, string seqname){
        try {
                string currentLevel = "";
                if(heirarchy != ""){
                        int pos = heirarchy.find_first_of(';');
-                       currentLevel=heirarchy.substr(0,pos);
-                       if (pos != (heirarchy.length()-1)) {  heirarchy=heirarchy.substr(pos+1);  }
-                       else { heirarchy = ""; }
+                       
+                       if (pos == -1) { //you can't find another ;
+                               currentLevel = heirarchy;
+                               heirarchy = "";
+                               m->mothurOut(seqname + " is missing a ;, please check for other errors."); m->mothurOutEndLine();
+                       }else{
+                               currentLevel=heirarchy.substr(0,pos);
+                               if (pos != (heirarchy.length()-1)) {  heirarchy=heirarchy.substr(pos+1);  }
+                               else { heirarchy = ""; }
+                       }
+                       
                }
                return currentLevel;
        }
@@ -228,16 +236,16 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
                
                tree[0].accessions.push_back(seqName);
                string taxon;// = getNextTaxon(seqTaxonomy);
-               
+       
                while(seqTaxonomy != ""){
                        
                        level++;
-                       
+               
                        if (m->control_pressed) { return 0; }
                        
                        //somehow the parent is getting one too many accnos
                        //use print to reassign the taxa id
-                       taxon = getNextTaxon(seqTaxonomy);
+                       taxon = getNextTaxon(seqTaxonomy, seqName);
                        
                        if (taxon == "") {  m->mothurOut(seqName + " has an error in the taxonomy.  This may be due to a ;;"); m->mothurOutEndLine(); if (currentNode != 0) {  uniqueTaxonomies[currentNode] = currentNode; } break;  }
                        
@@ -254,21 +262,13 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
                                tree[currentNode].children[taxon] = numNodes-1;
                                tree[numNodes-1].parent = currentNode;
                                
-                               //                      int numChildren = tree[currentNode].children.size();
-                               //                      string heirarchyID = tree[currentNode].heirarchyID;
-                               //                      tree[currentNode].accessions.push_back(seqName);
-                               
                                currentNode = tree[currentNode].children[taxon];
                                tree[currentNode].accessions.push_back(seqName);
                                name2Taxonomy[seqName] = currentNode;
-                               //                      tree[currentNode].level = level;
-                               //                      tree[currentNode].childNumber = numChildren;
-                               //                      tree[currentNode].heirarchyID = heirarchyID + '.' + toString(tree[currentNode].childNumber);
                        }
        
                        if (seqTaxonomy == "") {   uniqueTaxonomies[currentNode] = currentNode; }
                }
-
        }
        catch(exception& e) {
                m->errorOut(e, "PhyloTree", "addSeqToTree");