1 #ifndef DISTANCECOMMAND_H
2 #define DISTANCECOMMAND_H
8 * Created by Sarah Westcott on 5/7/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
14 #include "command.hpp"
15 #include "validcalculator.h"
17 #include "sequencedb.h"
20 class DistanceCommand : public Command {
23 DistanceCommand(string);
37 string countends, output, fastafile, calc, outputDir, oldfastafile, column, compress;
39 int processors, numNewFasta;
41 map<int, int> processIDS; //end line, processid
42 vector<linePair*> lines;
45 vector<string> Estimators; //holds estimators to be used
47 //void m->appendFiles(string, string);
48 void createProcesses(string);
49 int driver(/*Dist*, SequenceDB, */int, int, string, float);
50 int driver(int, int, string, string);
53 int driverMPI(int, int, MPI_File&, float);
54 int driverMPI(int, int, string, unsigned long int&);
55 int driverMPI(int, int, string, unsigned long int&, string);
58 //int convertMatrix(string);
60 //int convertToLowerTriangle(string);