added help for heatmap.sim

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 9e703ceeb62c2d610776c7f245980de651ab28a1..17f1b3387ee1279a3b44e6ef3d34b732fc88834d 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,38 +11,33 @@
  */
 
 #include "command.hpp"
-#include "mothur.h"
 #include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-using namespace std;
+#include "sequence.hpp"
 
 class FilterSeqsCommand : public Command {
 
 public:
-       FilterSeqsCommand() {};
+       FilterSeqsCommand();
        ~FilterSeqsCommand() {};
        int execute();  
        
 private:
-       void doTrump();
+       void doHard();
+       void doTrump(Sequence);
+       void doVertical();
        void doSoft();
-       void doFilter();
-       
-       GlobalData* globaldata;
-       string filename, trump, filter;
-       
-       ReadFasta* readFasta;
-       ReadNexus* readNexus;
-       ReadClustal* readClustal;
-       ReadPhylip* readPhylip;
+       void getFreqs(Sequence);
+       string filter;  
+       int alignmentLength;
+
+       char trump;
+       bool vertical;
+       float soft;
+       int numSeqs;
        
-       vector<bool> columnsToRemove;
-       SequenceDB* db;
-       double soft;
+       GlobalData* globaldata; 
+       vector<int> a, t, g, c, gap;
+
 };
 
-#endif
\ No newline at end of file
+#endif