X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=5eb49d3802177bf998e8fe9d0ba1dd80c2828709;hb=30c1fd8c45b6f0d66c17f2714dbb58b8ddccdce2;hp=af4c03a950a0f42ad4fd9d7453ad698423381bd0;hpb=5b7ac70116137b52dd7884b76c5bca660a5fea38;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index af4c03a..5eb49d3 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,37 +11,44 @@
  */
 
 #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 doHard();
-	void doVertical();
-	
-	int alignmentLength;
+	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;
+	vector<int> bufferSizes;
+
+	char trump;
+	bool abort;
+	float soft;
 	int numSeqs;
 	
-	GlobalData* globaldata;	
-	ReadSeqs* readSeqs;
-	SequenceDB* db;
+	string createFilter();
+	int createProcessesCreateFilter(Filters&, string);
+	int driverCreateFilter(Filters&, string, linePair*);
+	int MPICreateFilter(Filters&, vector<string>&);	
+	int setLines(string);
+	int parseBuffer(string, vector<string>&);
 	
-	string filter;
-
 };
 
 #endif