pat's edits from 1/26/2010

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 3e4f6ad3b36f4a137ceef8cb774b905b238c2f20..473d4d11d78bed00e56a02472afeb4980e19e87e 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -200,8 +200,8 @@ int ClassifySeqsCommand::execute(){
        try {
                if (abort == true) {    return 0;       }
                
-               if(method == "bayesian")                        {       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);           }
-               else if(method == "knn")                        {       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted);                               }
+               if(method == "bayesian"){       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters);           }
+               else if(method == "knn"){       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted);                               }
                else {
                        mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
                        mothurOutEndLine();
@@ -380,7 +380,7 @@ string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
                //keep what you have counting the levels
                while (tax.find_first_of(';') != -1) {
                        //get taxon
-                       taxon = tax.substr(0,tax.find_first_of(';'));
+                       taxon = tax.substr(0,tax.find_first_of(';'))+';';
                        tax = tax.substr(tax.find_first_of(';')+1, tax.length());
                        newTax += taxon;
                        level++;
@@ -480,13 +480,14 @@ int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFNa
                        
                        if (candidateSeq->getName() != "") {
                                taxonomy = classify->getTaxonomy(candidateSeq);
-                               
+
                                if (taxonomy != "bad seq") {
                                        //output confidence scores or not
                                        if (probs) {
                                                outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
                                        }else{
                                                outTax << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
+                                               cout << classify->getSimpleTax() << endl;
                                        }
                                        
                                        outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;