X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=232b0acb9966c19d0dafe9a3875dbc702e925754;hb=5d176c0f8049654ec3ae5a869c9ee3cecb991dc6;hp=fffa45770cde70da74792b6bab1feb105b0bd1d5;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index fffa457..232b0ac 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -6,43 +6,44 @@
  *  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"
+#include "mpi.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;
+	struct linePair {
+		int start;
+		int numSeqs;
+		linePair(long int i, int j) : start(i), numSeqs(j) {}
+	};
+	vector<linePair*> lines;
+
+
+	string vertical, filter, fasta, hard, outputDir, filterFileName;
+	vector<string> fastafileNames;	
+	int alignmentLength, processors;
+
+	char trump;
+	bool abort;
+	float soft;
+	int numSeqs;
 	
-	vector<bool> columnsToRemove;
-	SequenceDB* db;
-	double soft;
+	string createFilter();
+	int createProcessesCreateFilter(Filters&, string);
+	int driverCreateFilter(Filters&, string, linePair*);
 };
 
-#endif
\ No newline at end of file
+#endif