X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=81b915efcbf97e4b91bfca3bf27353da8f9ea8e9;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hp=f88fe2c442cf1d8ea6b0457a45390383c0c45698;hpb=dc874a77f24b3808775e2ce7e39595c647a07f82;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index f88fe2c..81b915e 100644
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -11,27 +11,52 @@
  */
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-#include <set>
-
-using namespace std;
 
 class ScreenSeqsCommand : public Command {
 	
 public:
+	ScreenSeqsCommand(string);
 	ScreenSeqsCommand();
 	~ScreenSeqsCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
+	void help();
+	
 private:
-	void screenNameGroupFile(set<string>);
-	int numSeqs;	
-	GlobalData* globaldata;	
-	ReadSeqs* readSeqs;
-	SequenceDB* db;
+
+	struct linePair {
+		unsigned long int start;
+		unsigned long int end;
+		linePair(unsigned long int i, unsigned long int j) : start(i), end(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, set<string>&);
+	int createProcesses(string, string, string, set<string>&);
+	
+	#ifdef USE_MPI
+	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&, set<string>&);
+	#endif
+
+	bool abort;
+	string fastafile, namefile, groupfile, alignreport, outputDir;
+	int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
+	vector<string> outputNames;
+	vector<string> optimize;
+	map<string, vector<string> > outputTypes;
+	
+	int getSummary(vector<unsigned long int>&);
+	int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);
+	int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, linePair*);	
 };
 
 #endif