*** empty log message ***

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index af4c03a950a0f42ad4fd9d7453ad698423381bd0..924c36627fec65abd777c5ae530bf154583e954f 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,14 +11,12 @@
  */
 
 #include "command.hpp"
-#include "mothur.h"
 #include "globaldata.hpp"
 #include "readfasta.h"
 #include "readnexus.h"
 #include "readclustal.h"
 #include "readseqsphylip.h"
 
-using namespace std;
 
 class FilterSeqsCommand : public Command {
 
@@ -28,19 +26,20 @@ public:
        int execute();  
        
 private:
-       void doTrump();
-       void doSoft();
        void doHard();
-       void doVertical();
-       
+       void doTrump(Sequence);
+       void doSoft(Sequence);
+       void doVertical(Sequence);
+       string filter;  
        int alignmentLength;
-       int numSeqs;
+
+       char trump;
+       bool vertical;
        
        GlobalData* globaldata; 
-       ReadSeqs* readSeqs;
-       SequenceDB* db;
+//     ReadSeqs* readSeqs;
+//     SequenceDB* db;
        
-       string filter;
 
 };