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);
26 vector<string> getRequiredParameters();
27 vector<string> getValidParameters();
28 vector<string> getRequiredFiles();
29 map<string, vector<string> > getOutputFiles() { return outputTypes; }
43 string countends, output, fastafile, calc, outputDir, oldfastafile, column, compress;
45 int processors, numNewFasta;
47 vector<int> processIDS; //end line, processid
48 vector<distlinePair> lines;
51 vector<string> Estimators, outputNames; //holds estimators to be used
52 map<string, vector<string> > outputTypes;
54 //void m->appendFiles(string, string);
55 void createProcesses(string);
56 int driver(/*Dist*, SequenceDB, */int, int, string, float);
57 int driver(int, int, string, string);
60 int driverMPI(int, int, MPI_File&, float);
61 int driverMPI(int, int, string, unsigned long int&);
62 int driverMPI(int, int, string, unsigned long int&, string);
65 //int convertMatrix(string);
67 //int convertToLowerTriangle(string);