added save parameter to align.seqs, chimera commands, classify.seqs, and seq.error...

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 9c8dbcac9caf436fcf44b2c416a9e063509561aa..3dbf06ee5bf18c5f6c5ee96e717ec4348c919310 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "classify.h"
+#include "referencedb.h"
 
 //KNN and Bayesian methods modeled from algorithms in
 //Naı¨ve Bayesian Classifier for Rapid Assignment of rRNA Sequences 
@@ -60,11 +61,12 @@ private:
        map<string,  vector<string> >::iterator itNames;
        
        Classify* classify;
+       ReferenceDB* rdb;
        
        string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
        int processors, kmerSize, numWanted, cutoff, iters;
        float match, misMatch, gapOpen, gapExtend;
-       bool abort, probs;
+       bool abort, probs, save;
        
        int driver(linePair*, string, string, string);
        void appendTaxFiles(string, string);