X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=611cbbc1b226c13d859273dc0cb356bb3b3d13d5;hb=7e354c9abb09ea3cf5b500a16cc7f6dd79ccb6f5;hp=b59d0a4b4cfa1ce7f7d86deb48b90515f5cc965a;hpb=544469443afe44920bdf279aefd26d29534cabaf;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index b59d0a4..611cbbc 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,37 +11,29 @@
  */
 
 #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 doHard();
-	void doVertical();
-	string filter;	
+	string vertical, filter, fastafile, hard;	
 	int alignmentLength;
 
 	char trump;
-	bool vertical;
-	
-	GlobalData* globaldata;	
-//	ReadSeqs* readSeqs;
-//	SequenceDB* db;
+	bool abort;
+	float soft;
+	int numSeqs;
 	
+	Filters F;
+		
+	vector<int> a, t, g, c, gap;
 
 };