X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.h;h=602326c42e2ff75afbeb8050479cf7e188b8b634;hb=77ac47e1ea0b5a0c6f55eb25e6bc7d7494ed3ad2;hp=9b987261d10cc62f5296d1717752eb5d7c587dae;hpb=faf4e99552d6fb4595ff348b1f909ddc74536da2;p=mothur.git

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 9b98726..602326c 100644
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -11,19 +11,57 @@
  */
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
 
 class ScreenSeqsCommand : public Command {
 	
 public:
+	ScreenSeqsCommand(string);
 	ScreenSeqsCommand();
-	~ScreenSeqsCommand();
-	int execute();
+	~ScreenSeqsCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "screen.seqs";				}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getHelpString();	
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+	
 private:
-	void screenNameGroupFile(set<string>);
-	void screenGroupFile(set<string>);
 
-	GlobalData* globaldata;	
+	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 screenQual(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, qualfile;
+	int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
+	vector<string> outputNames;
+	vector<string> optimize;
+	map<string, int> nameMap;
+	int readNames();
+	
+	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