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"
16 #include "validcalculator.h"
18 class RareFactSharedCommand : public Command {
21 RareFactSharedCommand(string);
22 RareFactSharedCommand();
23 ~RareFactSharedCommand() {}
25 vector<string> setParameters();
26 string getCommandName() { return "rarefaction.shared"; }
27 string getCommandCategory() { return "OTU-Based Approaches"; }
28 string getHelpString();
29 string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.shared"; }
32 void help() { m->mothurOut(getHelpString()); }
37 vector<SharedRAbundVector*> lookup;
40 vector<Display*> rDisplays;
45 bool abort, allLines, jumble;
46 set<string> labels; //holds labels to be used
47 string label, calc, groups, outputDir, sharedfile;
48 vector<string> Estimators, Groups, outputNames;