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 {
29 ~DistanceCommand() {};
33 GlobalData* globaldata;
34 ValidCalculators* validCalculator;
37 ofstream out, phylipOut;
39 string outputFileName;
40 string countends, phylip;
43 map<int, int> processIDS; //end line, processid
44 map<int, int>::iterator it;
45 vector<linePair*> lines;
47 void appendFiles(string, string);
48 void createProcesses(string, string);
49 int driver(Dist*, SequenceDB*, int, int, string, string, float);