modified trim.seqs command

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 0a34ff303e618839e3fd80583e91f9ab10305ff8..565d5283329124a65aca975d51a9588cb791670d 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "globaldata.hpp"
+#include "sequence.hpp"
 
 class TrimSeqsCommand : public Command {
 public:
@@ -27,18 +28,15 @@ private:
        bool stripReverse(Sequence&);
        
        GlobalData* globaldata;
-       
-       int totalBarcodeCount, matchBarcodeCount;
-       int totalFPrimerCount, matchFPrimerCount;
-       int totalRPrimerCount, matchRPrimerCount;
-       
+
+       int totalBarcodeCount, matchBarcodeCount; // to be removed
+       int totalFPrimerCount, matchFPrimerCount; // to be removed
+       int totalRPrimerCount, matchRPrimerCount; // to be removed
        
        bool oligos, flip;
-       int forwardPrimerMismatch, reversePrimerMismatch, barcodeMismatch;
        int numFPrimers, numRPrimers;
        vector<string> forPrimer, revPrimer;
        map<string, string> barcodes;
-
 };
 
 #endif