fixed some bugs

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 06eaa6db7e2deb8b74344d7f408f09734cbf43cf..6fe171a1ee7f3027377e0e02e6a78e2831a86a0b 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,35 +11,36 @@
  */
 
 #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 {
 
 public:
-       FilterSeqsCommand() {};
+       FilterSeqsCommand();
        ~FilterSeqsCommand() {};
        int execute();  
        
 private:
        void doTrump();
        void doSoft();
-       void doFilter();
-       
-       GlobalData* globaldata;
-       string filename, trump, filter;
+       void doHard();
+       void doVertical();
+       string filter;  
+       int alignmentLength;
+
+       char trump;
+       bool vertical;
        
-       ReadSeqs* readSeqs;
+       GlobalData* globaldata; 
+//     ReadSeqs* readSeqs;
+//     SequenceDB* db;
        
-       vector<bool> columnsToRemove;
-       SequenceDB* db;
-       double soft;
+
 };
 
-#endif
\ No newline at end of file
+#endif