added distance search method to classify.seqs

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 0255bd2409c043abfa1a7d261aa2910c78f9440e..19fc8a011d9b3dbc8dd8f1e482f7b50dc100078f 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -12,7 +12,7 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "alignment.hpp"
+//#include "alignment.hpp"
 #include "classify.h"
 
 //KNN and Bayesian methods modeled from algorithms in
@@ -48,7 +48,7 @@ private:
        
        Classify* classify;
        
-       string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName;
+       string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir;
        int processors, kmerSize, numWanted, cutoff, iters;
        float match, misMatch, gapOpen, gapExtend;
        bool abort, probs;