X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=bayesian.cpp;h=6f65965bfb912e983d4de12dcbaa3dfe307e23e1;hp=cf70010e76a6b9cba77b8ade2fcd7d18713391d3;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=006601d68abe8d0061f77e8d28323b160750e343

diff --git a/bayesian.cpp b/bayesian.cpp
index cf70010..6f65965 100644
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -298,7 +298,7 @@ string Bayesian::getTaxonomy(Sequence* seq) {
 			}  
 		}
 		
-		if (queryKmers.size() == 0) {  m->mothurOut(seq->getName() + "is bad."); m->mothurOutEndLine(); simpleTax = "unknown;";  return "unknown;"; }
+		if (queryKmers.size() == 0) {  m->mothurOut(seq->getName() + " is bad. It has no kmers of length " + toString(kmerSize) + "."); m->mothurOutEndLine(); simpleTax = "unknown;";  return "unknown;"; }
 		
 		
 		int index = getMostProbableTaxonomy(queryKmers);
@@ -308,7 +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;	
 	}
@@ -374,6 +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
@@ -383,11 +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);
 		}