1 #ifndef COLLECTSHAREDCOMMAND_H
2 #define COLLECTSHAREDCOMMAND_H
4 * collectsharedcommand.h
7 * Created by Sarah Westcott on 1/2/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
13 #include "command.hpp"
14 #include "sharedordervector.h"
15 #include "inputdata.h"
18 #include "validcalculator.h"
19 #include "sharedutilities.h"
22 class CollectSharedCommand : public Command {
25 CollectSharedCommand(string);
26 CollectSharedCommand();
27 ~CollectSharedCommand();
29 vector<string> setParameters();
30 string getCommandName() { return "collect.shared"; }
31 string getCommandCategory() { return "OTU-Based Approaches"; }
32 string getOutputFileNameTag(string, string);
33 string getHelpString();
34 string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.shared"; }
35 string getDescription() { return "generates collector's curves for calculators, which describe the similarity between communities or their shared richness"; }
38 void help() { m->mothurOut(getHelpString()); }
42 SharedOrderVector* order;
45 vector<Display*> cDisplays;
48 bool abort, allLines, all;
49 set<string> labels; //holds labels to be used
50 string label, calc, groups, outputDir, sharedfile;
51 vector<string> Estimators, Groups, outputNames;