X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=f1b72051250d07a389ed332b0690cbcda3b807c0;hb=cad05a21b084833b07808c1586e755be48fe7e1a;hp=56c9d82f1625a2a9481a203b7b217a9bc3b66bc4;hpb=544469443afe44920bdf279aefd26d29534cabaf;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 56c9d82..f1b7205 100644
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -11,25 +11,40 @@
  */
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-using namespace std;
 
 class ScreenSeqsCommand : public Command {
 	
 public:
-	ScreenSeqsCommand();
+	ScreenSeqsCommand(string);
 	~ScreenSeqsCommand();
 	int execute();
+	void help();
+	
 private:
-	void screenNameGroupFile(set<string>);
-	void screenGroupFile(set<string>);
 
-	GlobalData* globaldata;	
+	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, outputDir;
+	int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors;
+	vector<string> outputNames;
 };
 
 #endif