added design and sets parameters to the rarefaction.shared command. finished work...

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 0504e6635802c3f6e3e186e4568675906774b3ff..4e244905ff6b755fd064617368506b9160770048 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -467,7 +467,6 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
             }
                        
                }
-               
        }
        catch(exception& e) {
                m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
@@ -486,7 +485,7 @@ ClassifySeqsCommand::~ClassifySeqsCommand(){
 int ClassifySeqsCommand::execute(){
        try {
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
-               
+        
                if(method == "bayesian"){       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip);             }
                else if(method == "knn"){       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand());                               }
                else {
@@ -507,8 +506,8 @@ int ClassifySeqsCommand::execute(){
                        string RippedTaxName = m->getRootName(m->getSimpleName(baseTName));
                        RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
                        if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
-                       RippedTaxName +=  "."; 
-               
+                       if (RippedTaxName != "") { RippedTaxName +=  "."; }
+           
                        if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
                        string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
                        string newaccnosFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "flip.accnos";