removed line option

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 17f1b3387ee1279a3b44e6ef3d34b732fc88834d..611cbbc1b226c13d859273dc0cb356bb3b3d13d5 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,31 +11,28 @@
  */
 
 #include "command.hpp"
-#include "globaldata.hpp"
-#include "sequence.hpp"
+#include "filters.h"
 
+class Sequence;
 class FilterSeqsCommand : public Command {
 
 public:
-       FilterSeqsCommand();
+       FilterSeqsCommand(string);
        ~FilterSeqsCommand() {};
        int execute();  
+       void help();
        
 private:
-       void doHard();
-       void doTrump(Sequence);
-       void doVertical();
-       void doSoft();
-       void getFreqs(Sequence);
-       string filter;  
+       string vertical, filter, fastafile, hard;       
        int alignmentLength;
 
        char trump;
-       bool vertical;
+       bool abort;
        float soft;
        int numSeqs;
        
-       GlobalData* globaldata; 
+       Filters F;
+               
        vector<int> a, t, g, c, gap;
 
 };