1 #ifndef RAREFACTCOMMAND_H
2 #define RAREFACTCOMMAND_H
7 * Created by Sarah Westcott on 1/2/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 #include "command.hpp"
13 #include "ordervector.hpp"
14 #include "inputdata.h"
17 #include "validcalculator.h"
19 class RareFactCommand : public Command {
22 RareFactCommand(string);
26 vector<string> setParameters();
27 string getCommandName() { return "rarefaction.single"; }
28 string getCommandCategory() { return "OTU-Based Approaches"; }
30 string getHelpString();
31 string getOutputPattern(string);
32 string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.single"; }
33 string getDescription() { return "generate intra-sample rarefaction curves using a re-sampling without replacement approach"; }
36 void help() { m->mothurOut(getHelpString()); }
40 vector<Display*> rDisplays;
44 int nIters, abund, processors, alpha;
47 bool abort, allLines, groupMode;
48 set<string> labels; //holds labels to be used
49 string label, calc, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
50 vector<string> Estimators;
51 vector<string> inputFileNames, outputNames;
52 vector<string> groups;
55 vector<string> parseSharedFile(string, map<string, set<int> >&);
56 vector<string> createGroupFile(vector<string>&, map<int, string>);