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 "globaldata.hpp"
16 #include "validcalculator.h"
18 #include "sequencedb.h"
25 class DistanceCommand : public Command {
28 DistanceCommand(string);
29 ~DistanceCommand() {};
34 GlobalData* globaldata;
35 ValidCalculators* validCalculator;
38 ofstream out, outFile;
40 string countends, phylip, fastafile, calc;
43 map<int, int> processIDS; //end line, processid
44 map<int, int>::iterator it;
45 vector<linePair*> lines;
48 map<string, string> parameters;
49 map<string, string>::iterator it2;
51 vector<string> Estimators; //holds estimators to be used
53 void appendFiles(string, string);
54 void createProcesses(string);
55 int driver(Dist*, SequenceDB*, int, int, string, float);