added pca command

[mothur.git] / bayesian.cpp

diff --git a/bayesian.cpp b/bayesian.cpp
index 5272b2d1761285f934e9e8e1a474fd27f1edc328..e6adfc24b863442a58edcd7f348c83f843b10635 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -11,8 +11,8 @@
 #include "kmer.hpp"
 
 /**************************************************************************************************/
-Bayesian::Bayesian(string tfile, string tempFile, string method, int ksize, int cutoff, bool p) : 
-Classify(tfile, tempFile, method, ksize, 0.0, 0.0, 0.0, 0.0), kmerSize(ksize), confidenceThreshold(cutoff), probs(p)  {
+Bayesian::Bayesian(string tfile, string tempFile, string method, int ksize, int cutoff, int i) : 
+Classify(tfile, tempFile, method, ksize, 0.0, 0.0, 0.0, 0.0), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
        try {
                                        
                numKmers = database->getMaxKmer() + 1;
@@ -116,18 +116,9 @@ string Bayesian::getTaxonomy(Sequence* seq) {
                int index = getMostProbableTaxonomy(queryKmers);
                                        
                //bootstrap - to set confidenceScore
-               if (probs) {
-                       int numToSelect = queryKmers.size() / 8;
-                       tax = bootstrapResults(queryKmers, index, numToSelect);
-               }else{
-                       TaxNode seqTax = phyloTree->get(index);
-                       while (seqTax.level != 0) { //while you are not at the root
-                               tax = seqTax.name + ";" + tax;
-                               seqTax = phyloTree->get(seqTax.parent);
-                       }
-                       simpleTax = tax;
-               }
-                               
+               int numToSelect = queryKmers.size() / 8;
+               tax = bootstrapResults(queryKmers, index, numToSelect);
+                                               
                return tax;     
        }
        catch(exception& e) {
@@ -151,7 +142,7 @@ string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
                map<string, int>::iterator itBoot2;
                map<int, int>::iterator itConvert;
                
-               for (int i = 0; i < 100; i++) {
+               for (int i = 0; i < iters; i++) {
                        vector<int> temp;
                                                
                        for (int j = 0; j < numToSelect; j++) {