optimizing classify.seqs calculating of template probabilities.

[mothur.git] / bayesian.cpp

diff --git a/bayesian.cpp b/bayesian.cpp
index bccf0ce0dda18501c129b7604546f4e9fc43382b..49be4af57ff66f46ac04912535d7918518cc75d2 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -64,7 +64,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
                        }
                        saveIn.close();                 
                }
-FilesGood = false;
+
                if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood){       
                        if (tempFile == "saved") { m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory.");     m->mothurOutEndLine(); }
                        
@@ -143,7 +143,6 @@ FilesGood = false;
                                        }
                                #endif
 
-                               
                                //for each word
                                for (int i = 0; i < numKmers; i++) {
                                        if (m->control_pressed) {  break; }
@@ -162,12 +161,10 @@ FilesGood = false;
                                        
                                        vector<int> seqsWithWordi = database->getSequencesWithKmer(i);
                                        
-                                       map<int, int> count;
-                                       for (int k = 0; k < genusNodes.size(); k++) {  count[genusNodes[k]] = 0;  }                     
-                                                       
                                        //for each sequence with that word
+                    vector<int> count; count.resize(genusNodes.size(), 0);
                                        for (int j = 0; j < seqsWithWordi.size(); j++) {
-                                               int temp = phyloTree->getIndex(names[seqsWithWordi[j]]);
+                                               int temp = phyloTree->getGenusIndex(names[seqsWithWordi[j]]);
                                                count[temp]++;  //increment count of seq in this genus who have this word
                                        }
                                        
@@ -181,9 +178,9 @@ FilesGood = false;
                                                //probabilityInThisTaxonomy = (# of seqs with that word in this taxonomy + probabilityInTemplate) / (total number of seqs in this taxonomy + 1);
                                                
                                                
-                                               wordGenusProb[i][k] = log((count[genusNodes[k]] + probabilityInTemplate) / (float) (genusTotals[k] + 1));  
+                                               wordGenusProb[i][k] = log((count[k] + probabilityInTemplate) / (float) (genusTotals[k] + 1));  
                                                                        
-                                               if (count[genusNodes[k]] != 0) { 
+                                               if (count[k] != 0) { 
                                                        #ifdef USE_MPI
                                                                int pid;
                                                                MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are