Fixes bug with classify.seqs

#307

Mothur.xcodeproj/project.pbxproj

@@ -3384,8 +3384,8 @@
 				GCC_MODEL_TUNING = G5;
 				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
-					"VERSION=\"\\\"1.39.1\\\"\"",
-					"RELEASE_DATE=\"\\\"2/2/2017\\\"\"",
+					"VERSION=\"\\\"1.39.2\\\"\"",
+					"RELEASE_DATE=\"\\\"2/16/2017\\\"\"",
 					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
 				);
 				GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
@@ -3419,8 +3419,8 @@
 				GCC_MODEL_TUNING = G5;
 				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
-					"VERSION=\"\\\"1.39.1\\\"\"",
-					"RELEASE_DATE=\"\\\"2/2/2017\\\"\"",
+					"VERSION=\"\\\"1.39.2\\\"\"",
+					"RELEASE_DATE=\"\\\"2/16/2017\\\"\"",
 					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
 				);
 				GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
@@ -3505,8 +3505,8 @@
 				GCC_MODEL_TUNING = "";
 				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
-					"VERSION=\"\\\"1.39.1\\\"\"",
-					"RELEASE_DATE=\"\\\"2/2/2017\\\"\"",
+					"VERSION=\"\\\"1.39.2\\\"\"",
+					"RELEASE_DATE=\"\\\"2/16/2017\\\"\"",
 					"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
 				);
 				GCC_VERSION = "";

source/classifier/classify.cpp

@@ -123,26 +123,16 @@ int Classify::readTaxonomy(string file) {
 		phyloTree = new PhyloTree();
 		string name, taxInfo;
 		
-		m->mothurOutEndLine();
-		m->mothurOut("Reading in the " + file + " taxonomy...\t");	cout.flush();
+		m->mothurOut("\nReading in the " + file + " taxonomy...\t");	cout.flush();
         if (m->debug) { m->mothurOut("[DEBUG]: Taxonomies read in...\n"); }
         
-        
         taxonomy.clear(); 
         m->readTax(file, taxonomy, true);
         
-        //commented out to save time with large templates. 6/12/13
-        //map<string, string> tempTaxonomy;
-        for (map<string, string>::iterator itTax = taxonomy.begin(); itTax != taxonomy.end(); itTax++) {  
-            //if (m->inUsersGroups(itTax->first, names)) {
-                phyloTree->addSeqToTree(itTax->first, itTax->second);
+        for (map<string, string>::iterator itTax = taxonomy.begin(); itTax != taxonomy.end(); itTax++) {
+            phyloTree->addSeqToTree(itTax->first, itTax->second);
             if (m->control_pressed) { break; }
-                //tempTaxonomy[itTax->first] = itTax->second;
-           // }else {
-            //    m->mothurOut("[WARNING]: " + itTax->first + " is in your taxonomy file and not in your reference file, ignoring.\n");
-            //}
         }
-        //taxonomy = tempTaxonomy;
 
 		phyloTree->assignHeirarchyIDs(0);
         

source/classifier/phylotree.cpp

@@ -21,6 +21,7 @@ PhyloTree::PhyloTree(){
         tree[0].level = 0;
 		maxLevel = 0;
 		calcTotals = true;
+        
 		addSeqToTree("unknown", "unknown;");
 	}
 	catch(exception& e) {
@@ -92,16 +93,15 @@ PhyloTree::PhyloTree(string tfile){
             temp.erase(itTemp++);
         }
         
-		assignHeirarchyIDs(0);
-        
         string unknownTax = "unknown;";
         //added last taxon until you get desired level
 		for (int i = 1; i < maxLevel; i++) {
 			unknownTax += "unknown_unclassfied;";
 		}
-        
         addSeqToTree("unknown", unknownTax);
         
+        assignHeirarchyIDs(0);
+        
 		//create file for summary if needed
 		setUp(tfile);
 	}
@@ -193,8 +193,7 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
 		
 		tree[0].accessions.push_back(seqName);
 		m->removeConfidences(seqTaxonomy);
-		
-		string taxon;// = getNextTaxon(seqTaxonomy);
+        string taxon;// = getNextTaxon(seqTaxonomy);
 	
 		while(seqTaxonomy != ""){
 			
@@ -219,12 +218,13 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
 			}
 			else{											//otherwise, create it
 				tree.push_back(TaxNode(taxon));
-				numNodes++;
-				tree[currentNode].children[taxon] = numNodes-1;
-                tree[currentNode].level = level;
-				tree[numNodes-1].parent = currentNode;
 				
-				currentNode = tree[currentNode].children[taxon];
+				tree[currentNode].children[taxon] = numNodes;
+                tree[numNodes].level = level;
+				tree[numNodes].parent = currentNode;
+                currentNode = numNodes;
+                numNodes++;
+				
 				tree[currentNode].accessions.push_back(seqName);
 				name2Taxonomy[seqName] = currentNode;
 			}
@@ -377,12 +377,12 @@ void PhyloTree::binUnclassified(string file){
 				}
 				else{											//otherwise, create it
 					copy.push_back(TaxNode(taxon));
-					copyNodes++;
-					copy[currentNode].children[taxon] = copyNodes-1;
-					copy[copyNodes-1].parent = currentNode;
-					copy[copyNodes-1].level = copy[currentNode].level + 1;
-									
-					currentNode = copy[currentNode].children[taxon];
+					
+					copy[currentNode].children[taxon] = copyNodes;
+					copy[copyNodes].parent = currentNode;
+					copy[copyNodes].level = copy[currentNode].level + 1;
+                    currentNode = copyNodes;
+                    copyNodes++;
 				}
 			}
 		}