- 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<unsigned long int>&, set<string>&);
+ #endif
+