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;
38 int processors, numNewFasta;
40 map<int, int> processIDS; //end line, processid
41 vector<linePair*> lines;
44 vector<string> Estimators; //holds estimators to be used
46 //void appendFiles(string, string);
47 void createProcesses(string);
48 int driver(/*Dist*, SequenceDB, */int, int, string, float);
51 int driverMPI(int, int, MPI_File&, float);
52 int driverMPI(int, int, string, long&);
55 int convertMatrix(string);
57 int convertToLowerTriangle(string);