changes while testing

[mothur.git] / bayesian.cpp

diff --git a/bayesian.cpp b/bayesian.cpp
index 6eaab6f2f974f8e1036561c2f76d9587d6dd0399..8278afb32e1d2c028a83ffdece17ed9910a78e20 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -145,6 +145,8 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
 
                                //for each word
                                for (int i = 0; i < numKmers; i++) {
+                    //m->mothurOut("[DEBUG]: kmer = " + toString(i) + "\n");
+                    
                                        if (m->control_pressed) {  break; }
                                        
                                        #ifdef USE_MPI
@@ -239,7 +241,9 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
                        }
                }
                
+        if (m->debug) { m->mothurOut("[DEBUG]: about to generateWordPairDiffArr\n"); }
                generateWordPairDiffArr();
+        if (m->debug) { m->mothurOut("[DEBUG]: done generateWordPairDiffArr\n"); }
                
                //save probabilities
                if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; }
@@ -298,7 +302,7 @@ 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);