X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=314e6617f6b2ec76033636ec8a05f722b3274e49;hb=d01397212a287495d3d0ec00beea93759bf25402;hp=97b36155af670c3d038c882e742356a1c6ee9a03;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 97b3615..314e661 100644
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -11,7 +11,6 @@
  */
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
 
 class ScreenSeqsCommand : public Command {
 	
@@ -22,16 +21,30 @@ public:
 	void help();
 	
 private:
-	void screenNameGroupFile(set<string>);
-	void screenGroupFile(set<string>);
 
-	GlobalData* globaldata;	
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
+	struct linePair {
+		unsigned long int start;
+		int numSeqs;
+		linePair(unsigned 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;
-	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