X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=f1b72051250d07a389ed332b0690cbcda3b807c0;hb=5412970cac5fbb63312d4dd279851f0482787901;hp=269275d38409c251ef3f9b0b1c2552602367f348;hpb=e7729bb337cfefcaba24549092cc89b44002af39;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 269275d..f1b7205 100644
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -21,13 +21,30 @@ public:
 	void help();
 	
 private:
-	void screenNameGroupFile(set<string>);
-	void screenGroupFile(set<string>);
-	void screenAlignReport(set<string>);
+
+	struct linePair {
+		int start;
+		int numSeqs;
+		linePair(long int i, int j) : start(i), numSeqs(j) {}
+	};
+	vector<int> processIDS;   //processid
+	vector<linePair*> lines;
+
+	int screenNameGroupFile(set<string>);
+	int screenGroupFile(set<string>);
+	int screenAlignReport(set<string>);
 	
+	int driver(linePair*, string, string, string, string, set<string>&);
+	int createProcesses(string, string, string, string, set<string>&);
+	
+	#ifdef USE_MPI
+	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<long>&, set<string>&);
+	#endif
+
 	bool abort;
-	string fastafile, namefile, groupfile, alignreport;
-	int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength;
+	string fastafile, namefile, groupfile, alignreport, outputDir;
+	int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors;
+	vector<string> outputNames;
 };
 
 #endif