added help for heatmap.sim

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index b59d0a4b4cfa1ce7f7d86deb48b90515f5cc965a..17f1b3387ee1279a3b44e6ef3d34b732fc88834d 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,14 +11,8 @@
  */
 
 #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 {
 
@@ -28,20 +22,21 @@ public:
        int execute();  
        
 private:
-       void doTrump();
-       void doSoft();
        void doHard();
+       void doTrump(Sequence);
        void doVertical();
+       void doSoft();
+       void getFreqs(Sequence);
        string filter;  
        int alignmentLength;
 
        char trump;
        bool vertical;
+       float soft;
+       int numSeqs;
        
        GlobalData* globaldata; 
-//     ReadSeqs* readSeqs;
-//     SequenceDB* db;
-       
+       vector<int> a, t, g, c, gap;
 
 };