changes while testing 1.27

[mothur.git] / bayesian.cpp

diff --git a/bayesian.cpp b/bayesian.cpp
index f7ea6e4351868a20a191169b995e94faff6fa053..1dc38337aef1bcc3b695ff56e86061cdab58c13d 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -27,7 +27,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
                if (baseTName == "saved") { baseTName = rdb->getSavedTaxonomy(); }
                
                /************calculate the probablity that each word will be in a specific taxonomy*************/
-               string tfileroot = baseTName.substr(0,baseTName.find_last_of(".")+1);
+               string tfileroot = m->getFullPathName(baseTName.substr(0,baseTName.find_last_of(".")+1));
                string tempfileroot = m->getRootName(m->getSimpleName(baseName));
                string phyloTreeName = tfileroot + "tree.train";
                string phyloTreeSumName = tfileroot + "tree.sum";
@@ -111,10 +111,9 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
                                //initialze probabilities
                                wordGenusProb.resize(numKmers);
                                WordPairDiffArr.resize(numKmers);
-                       //cout << numKmers << '\t' << genusNodes.size() << endl;
+                       
                                for (int j = 0; j < wordGenusProb.size(); j++) {        wordGenusProb[j].resize(genusNodes.size());             }
-                       //cout << numKmers << '\t' << genusNodes.size() << endl;        
-                               ofstream out;
+                    ofstream out;
                                ofstream out2;
                                
                                #ifdef USE_MPI
@@ -231,7 +230,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
                                delete phyloTree;
                                
                                phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
-                               
+                
                                //save probabilities
                                if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; }
                        }
@@ -505,7 +504,7 @@ map<string, int> Bayesian::parseTaxMap(string newTax) {
                exit(1);
        }
 }
-/**************************************************************************************************/
+**************************************************************************************************/
 void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string inNumName) {
        try{
                
@@ -606,7 +605,7 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
                                istringstream iss (tempBuf,istringstream::in);
                                float probTemp;
                                iss >> zeroCountProb[i] >> numbers[i] >> probTemp; 
-                               WordPairDiffArr[i].prob = tempProb;
+                               WordPairDiffArr[i].prob = probTemp;
 
                        }