class DistanceCommand : public Command {
public:
- DistanceCommand(string);
+ DistanceCommand(string);
~DistanceCommand();
int execute();
void help();
Dist* distCalculator;
SequenceDB alignDB;
- string countends, phylip, fastafile, calc, outputDir;
+ string countends, output, fastafile, calc, outputDir;
int processors;
float cutoff;
map<int, int> processIDS; //end line, processid
//void appendFiles(string, string);
void createProcesses(string);
int driver(/*Dist*, SequenceDB, */int, int, string, float);
+
+ #ifdef USE_MPI
+ int driverMPI(int, int, MPI_File&, float);
+ int driverMPI(int, int, string, long&);
+ #endif
+
+ int convertMatrix(string);
+ int convertToLowerTriangle(string);
};