X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=3c46036468401352987fb9d6cb61b48447613dab;hb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba;hp=17f1b3387ee1279a3b44e6ef3d34b732fc88834d;hpb=faf4e99552d6fb4595ff348b1f909ddc74536da2;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 17f1b33..3c46036 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,33 +11,51 @@
  */
 
 #include "command.hpp"
-#include "globaldata.hpp"
-#include "sequence.hpp"
+#include "filters.h"
+#include "mpi.h"
 
+class Sequence;
 class FilterSeqsCommand : public Command {
 
 public:
-	FilterSeqsCommand();
+	FilterSeqsCommand(string);
 	~FilterSeqsCommand() {};
 	int execute();	
+	void help();
 	
 private:
-	void doHard();
-	void doTrump(Sequence);
-	void doVertical();
-	void doSoft();
-	void getFreqs(Sequence);
-	string filter;	
-	int alignmentLength;
+	struct linePair {
+		int start;
+		int num;
+		linePair(long int i, long int j) : start(i), num(j) {}
+	};
+	vector<linePair*> lines;
+	vector<int> processIDS;
+
+	string vertical, filter, fasta, hard, outputDir, filterFileName;
+	vector<string> fastafileNames;	
+	int alignmentLength, processors;
+	vector<int> bufferSizes;
+	vector<string> outputNames;
 
 	char trump;
-	bool vertical;
+	bool abort;
 	float soft;
 	int numSeqs;
 	
-	GlobalData* globaldata;	
-	vector<int> a, t, g, c, gap;
-
+	string createFilter();
+	int filterSequences();
+	int createProcessesCreateFilter(Filters&, string);
+	int createProcessesRunFilter(string, string);
+	int driverRunFilter(string, string, string, linePair*);
+	int driverCreateFilter(Filters& F, string filename, linePair* line);
+	#ifdef USE_MPI
+	int driverMPIRun(int, int, MPI_File&, MPI_File&, vector<long>&);
+	int MPICreateFilter(int, int, Filters&, MPI_File&, vector<long>&);	
+	#endif
+	int setLines(string);
+	
+	
 };
 
 #endif