some changes while testing 1.9

[mothur.git] / bayesian.cpp

diff --git a/bayesian.cpp b/bayesian.cpp
index af1fa27f2202de76086e562c775229f4f241e387..b007c006dc741c2fd1755d60dcee7d3f5942aa39 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -33,11 +33,11 @@ Classify(tfile, tempFile, method, ksize, 0.0, 0.0, 0.0, 0.0), kmerSize(ksize), c
                
                /************calculate the probablity that each word will be in a specific taxonomy*************/
                ofstream out;
-               string probFileName = tempFile.substr(0,tempFile.find_last_of(".")+1) + char('0'+ kmerSize) + "mer.prob";
+               string probFileName = tfile.substr(0,tfile.find_last_of(".")+1) + tempFile.substr(0,tempFile.find_last_of(".")+1) + char('0'+ kmerSize) + "mer.prob";
                ifstream probFileTest(probFileName.c_str());
                
                ofstream out2;
-               string probFileName2 = tempFile.substr(0,tempFile.find_last_of(".")+1) + char('0'+ kmerSize) + "mer.numNonZero";
+               string probFileName2 = tfile.substr(0,tfile.find_last_of(".")+1) + tempFile.substr(0,tempFile.find_last_of(".")+1) + char('0'+ kmerSize) + "mer.numNonZero";
                ifstream probFileTest2(probFileName2.c_str());
                
                int start = time(NULL);
@@ -106,15 +106,21 @@ string Bayesian::getTaxonomy(Sequence* seq) {
                //get words contained in query
                //getKmerString returns a string where the index in the string is hte kmer number 
                //and the character at that index can be converted to be the number of times that kmer was seen
+
                string queryKmerString = kmer.getKmerString(seq->getUnaligned()); 
+
                vector<int> queryKmers;
                for (int i = 0; i < queryKmerString.length(); i++) {
                        if (queryKmerString[i] != '!') { //this kmer is in the query
                                queryKmers.push_back(i);
+ 
                        }
                }
-       
+               
+               if (queryKmers.size() == 0) {  m->mothurOut(seq->getName() + "is bad."); m->mothurOutEndLine(); return "bad seq"; }
+               
                int index = getMostProbableTaxonomy(queryKmers);
+
                
                if (m->control_pressed) { return tax; }
                                        
@@ -171,9 +177,10 @@ string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
                                }else{
                                        confidenceScores[taxonomy.level][taxonomy.name]++;
                                }
-                       
+               
                                taxonomy = phyloTree->get(taxonomy.parent);
                        }
+       
                }
                
                string confidenceTax = "";
@@ -181,7 +188,7 @@ string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
                TaxNode seqTax = phyloTree->get(tax);
                
                while (seqTax.level != 0) { //while you are not at the root
-                               
+                                       
                                itBoot2 = confidenceScores[seqTax.level].find(seqTax.name); //is this a classification we already have a count on
                                
                                int confidence = 0;
@@ -197,6 +204,7 @@ string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
                                seqTax = phyloTree->get(seqTax.parent);
                }
                
+               if (confidenceTax == "") { confidenceTax = "unclassified;"; simpleTax = "unclassified;"; }
                return confidenceTax;
                
        }
@@ -208,12 +216,11 @@ string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
 /**************************************************************************************************/
 int Bayesian::getMostProbableTaxonomy(vector<int> queryKmer) {
        try {
-               int indexofGenus;
+               int indexofGenus = 0;
                
                double maxProbability = -1000000.0;
                //find taxonomy with highest probability that this sequence is from it
                for (int k = 0; k < genusNodes.size(); k++) {
-               
                        //for each taxonomy calc its probability
                        double prob = 1.0;
                        for (int i = 0; i < queryKmer.size(); i++) {