Dist* distCalculator;
SequenceDB alignDB;
- string countends, output, fastafile, calc, outputDir;
- int processors;
+ string countends, output, fastafile, calc, outputDir, oldfastafile, column, compress;
+
+ int processors, numNewFasta;
float cutoff;
map<int, int> processIDS; //end line, processid
vector<linePair*> lines;
bool abort;
vector<string> Estimators; //holds estimators to be used
- //void appendFiles(string, string);
+ //void m->appendFiles(string, string);
void createProcesses(string);
int driver(/*Dist*, SequenceDB, */int, int, string, float);
- int driverMPI(int, int, string&, float);
+ int driver(int, int, string, string);
+
+ #ifdef USE_MPI
+ int driverMPI(int, int, MPI_File&, float);
+ int driverMPI(int, int, string, unsigned long int&);
+ int driverMPI(int, int, string, unsigned long int&, string);
+ #endif
- int convertMatrix(string);
+ //int convertMatrix(string);
+ bool sanityCheck();
+ //int convertToLowerTriangle(string);
};