*/
#include "mothur.h"
#include "command.hpp"
-#include "globaldata.hpp"
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>);
- 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 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