1 #ifndef RAREFACTSHAREDCOMMAND_H
2 #define RAREFACTSHAREDCOMMAND_H
4 * rarefactsharedcommand.h
7 * Created by Sarah Westcott on 1/6/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 #include "command.hpp"
13 #include "inputdata.h"
17 #include "validcalculator.h"
21 class RareFactSharedCommand : public Command {
24 RareFactSharedCommand(string);
25 RareFactSharedCommand();
26 ~RareFactSharedCommand();
27 vector<string> getRequiredParameters();
28 vector<string> getValidParameters();
29 vector<string> getRequiredFiles();
30 map<string, vector<string> > getOutputFiles() { return outputTypes; }
35 GlobalData* globaldata;
37 vector<SharedRAbundVector*> lookup;
39 ValidCalculators* validCalculator;
41 vector<Display*> rDisplays;
46 bool abort, allLines, jumble;
47 set<string> labels; //holds labels to be used
48 string label, calc, groups, outputDir;
49 vector<string> Estimators, Groups, outputNames;
50 map<string, vector<string> > outputTypes;