X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=1d2526fdca83114dcca76217917324d134bcc391;hb=aba5f8811829037b0a3004ef33f0ad4ed5e5fcf8;hp=232b0acb9966c19d0dafe9a3875dbc702e925754;hpb=5d176c0f8049654ec3ae5a869c9ee3cecb991dc6;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 232b0ac..1d2526f 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -26,15 +26,17 @@ public:
 private:
 	struct linePair {
 		int start;
-		int numSeqs;
-		linePair(long int i, int j) : start(i), numSeqs(j) {}
+		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 abort;
@@ -42,8 +44,16 @@ private:
 	int numSeqs;
 	
 	string createFilter();
+	int filterSequences();
 	int createProcessesCreateFilter(Filters&, string);
+	int createProcessesRunFilter(string, string);
 	int driverCreateFilter(Filters&, string, linePair*);
+	int driverRunFilter(string, string, string, linePair*);	
+	int driverMPIRun(istringstream&, MPI_File&);
+	int MPICreateFilter(Filters&, string);	
+	int setLines(string);
+	int parseBuffer(string, vector<string>&);
+	
 };
 
 #endif