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"; }
29 string getOutputFileNameTag(string, string);
30 string getHelpString();
31 string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.single"; }
32 string getDescription() { return "generate intra-sample rarefaction curves using a re-sampling without replacement approach"; }
35 void help() { m->mothurOut(getHelpString()); }
39 vector<Display*> rDisplays;
43 int nIters, abund, processors;
46 bool abort, allLines, groupMode;
47 set<string> labels; //holds labels to be used
48 string label, calc, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
49 vector<string> Estimators;
50 vector<string> inputFileNames, outputNames;
51 vector<string> groups;
54 vector<string> parseSharedFile(string, map<string, set<int> >&);
55 vector<string> createGroupFile(vector<string>&, map<int, string>);