X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=611cbbc1b226c13d859273dc0cb356bb3b3d13d5;hb=7b3c9ca940891c1b20b3b7ec13e05d7e7b316b63;hp=06eaa6db7e2deb8b74344d7f408f09734cbf43cf;hpb=d5d2761f88b41f1006d0b700e0ab51e2ce48b875;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 06eaa6d..611cbbc 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,35 +11,30 @@
  */
 
 #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 "filters.h"
 
+class Sequence;
 class FilterSeqsCommand : public Command {
 
 public:
-	FilterSeqsCommand() {};
+	FilterSeqsCommand(string);
 	~FilterSeqsCommand() {};
 	int execute();	
+	void help();
 	
 private:
-	void doTrump();
-	void doSoft();
-	void doFilter();
-	
-	GlobalData* globaldata;
-	string filename, trump, filter;
-	
-	ReadSeqs* readSeqs;
+	string vertical, filter, fastafile, hard;	
+	int alignmentLength;
+
+	char trump;
+	bool abort;
+	float soft;
+	int numSeqs;
 	
-	vector<bool> columnsToRemove;
-	SequenceDB* db;
-	double soft;
+	Filters F;
+		
+	vector<int> a, t, g, c, gap;
+
 };
 
-#endif
\ No newline at end of file
+#endif