finished work on classify.seqs bayesian method and various bug fixes

[mothur.git] / doTaxonomy.cpp

diff --git a/doTaxonomy.cpp b/doTaxonomy.cpp
index e66476415aca0f7d2b032e9be43845c7a3e561b6..06337b446bf0d79ffad7b29f4fb904c99f54058e 100644 (file)
--- a/doTaxonomy.cpp
+++ b/doTaxonomy.cpp
@@ -59,11 +59,13 @@ void PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
                if(childPointer != tree[currentNode].children.end()){   //if the node already exists, move on
                        currentNode = childPointer->second;
                        tree[currentNode].accessions.push_back(seqName);
+                       name2Taxonomy[seqName] = currentNode;
                }
                else{                                                                                   //otherwise, create it
                        tree.push_back(TaxNode(taxon));
                        numNodes++;
                        tree[currentNode].children[taxon] = numNodes-1;
+                       tree[numNodes-1].parent = currentNode;
 
 //                     int numChildren = tree[currentNode].children.size();
 //                     string heirarchyID = tree[currentNode].heirarchyID;
@@ -71,15 +73,30 @@ void PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
                        
                        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; }
+       }
+}
+/**************************************************************************************************/
+vector<int> PhyloTree::getGenusNodes() {
+       try {
+               genusIndex.clear();
+               //generate genusIndexes
+               map<int, int>::iterator it2;
+               for (it2=uniqueTaxonomies.begin(); it2!=uniqueTaxonomies.end(); it2++) {  genusIndex.push_back(it2->first);     }
+               
+               return genusIndex;
+       }
+       catch(exception& e) {
+               errorOut(e, "PhyloTree", "getGenusNodes");
+               exit(1);
        }
 }
-
 /**************************************************************************************************/
 
 void PhyloTree::assignHeirarchyIDs(int index){
@@ -92,9 +109,7 @@ void PhyloTree::assignHeirarchyIDs(int index){
                counter++;
                tree[it->second].level = tree[index].level + 1;
                assignHeirarchyIDs(it->second);
-
        }
-       
 }
 
 /**************************************************************************************************/