1 #ifndef HEATMAPSIMCOMMAND_H
2 #define HEATMAPSIMCOMMAND_H
8 * Created by Sarah Westcott on 6/8/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
13 #include "command.hpp"
14 #include "inputdata.h"
15 #include "validcalculator.h"
16 #include "heatmapsim.h"
17 #include "nameassignment.hpp"
19 class HeatMapSimCommand : public Command {
22 HeatMapSimCommand(string);
24 ~HeatMapSimCommand(){}
26 vector<string> setParameters();
27 string getCommandName() { return "heatmap.sim"; }
28 string getCommandCategory() { return "OTU-Based Approaches"; }
29 string getHelpString();
30 string getCitation() { return "http://www.mothur.org/wiki/Heatmap.sim"; }
33 void help() { m->mothurOut(getHelpString()); }
38 vector<SharedRAbundVector*> lookup;
39 vector<Calculator*> heatCalculators;
43 set<string> labels; //holds labels to be used
44 string format, groups, label, calc, sharedfile, phylipfile, columnfile, namefile, outputDir, inputfile;
45 vector<string> Estimators, Groups, outputNames;
47 int runCommandShared();