X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=bayesian.cpp;h=6eaab6f2f974f8e1036561c2f76d9587d6dd0399;hp=49be4af57ff66f46ac04912535d7918518cc75d2;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=159fd324dfecacb6617669246d85c787ae67f630

diff --git a/bayesian.cpp b/bayesian.cpp
index 49be4af..6eaab6f 100644
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -255,9 +255,8 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
 /**************************************************************************************************/
 Bayesian::~Bayesian() {
 	try {
-		
-		 delete phyloTree; 
-		 if (database != NULL) {  delete database; }
+        if (phyloTree != NULL) { delete phyloTree; }
+        if (database != NULL) {  delete database; }
 	}
 	catch(exception& e) {
 		m->errorOut(e, "Bayesian", "~Bayesian");
@@ -309,7 +308,11 @@ string Bayesian::getTaxonomy(Sequence* seq) {
 		//bootstrap - to set confidenceScore
 		int numToSelect = queryKmers.size() / 8;
 	
+        if (m->debug) {  m->mothurOut(seq->getName() + "\t"); }
+        
 		tax = bootstrapResults(queryKmers, index, numToSelect);
+        
+        if (m->debug) {  m->mothurOut("\n"); }
 		
 		return tax;	
 	}
@@ -375,6 +378,7 @@ string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
 		int seqTaxIndex = tax;
 		TaxNode seqTax = phyloTree->get(tax);
 		
+        
 		while (seqTax.level != 0) { //while you are not at the root
 					
 				itBoot2 = confidenceScores.find(seqTaxIndex); //is this a classification we already have a count on
@@ -384,11 +388,13 @@ string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
 					confidence = itBoot2->second;
 				}
 				
+                if (m->debug) { m->mothurOut(seqTax.name + "(" + toString(((confidence/(float)iters) * 100)) + ");"); }
+            
 				if (((confidence/(float)iters) * 100) >= confidenceThreshold) {
 					confidenceTax = seqTax.name + "(" + toString(((confidence/(float)iters) * 100)) + ");" + confidenceTax;
 					simpleTax = seqTax.name + ";" + simpleTax;
 				}
-				
+            
 				seqTaxIndex = seqTax.parent;
 				seqTax = phyloTree->get(seqTax.parent);
 		}