X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bayesian.cpp;h=1dc38337aef1bcc3b695ff56e86061cdab58c13d;hb=28bcfc4a41b8b82f66636587e0d4d355d07cbdd1;hp=f7ea6e4351868a20a191169b995e94faff6fa053;hpb=16abd6271c455bd01b34ff89a2e3641bef0fa128;p=mothur.git

diff --git a/bayesian.cpp b/bayesian.cpp
index f7ea6e4..1dc3833 100644
--- 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;
 
 			}