X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=0946396e3a0fe6623f3501feed5fc6e7b4ba239a;hb=9c23307c583d4e8595f75278c13e708788f2f058;hp=fffa45770cde70da74792b6bab1feb105b0bd1d5;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index fffa457..0946396 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -6,43 +6,35 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 5/4/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 #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;
-	
-	ReadFasta* readFasta;
-	ReadNexus* readNexus;
-	ReadClustal* readClustal;
-	ReadPhylip* readPhylip;
+	string vertical, filter, fastafile, hard, outputDir;	
+	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