X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.cpp;h=473d4d11d78bed00e56a02472afeb4980e19e87e;hb=c99f3846e7a7b6f06ab46508baa5409204ad6290;hp=3e4f6ad3b36f4a137ceef8cb774b905b238c2f20;hpb=ee4dd201fa4f2c4ede5b2e525c82cce0a37de363;p=mothur.git

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 3e4f6ad..473d4d1 100644
--- 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;