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"
16 #include "validcalculator.h"
17 #include "heatmapsim.h"
21 class HeatMapSimCommand : public Command {
24 HeatMapSimCommand(string);
27 vector<string> getRequiredParameters();
28 vector<string> getValidParameters();
29 vector<string> getRequiredFiles();
30 map<string, vector<string> > getOutputFiles() { return outputTypes; }
35 GlobalData* globaldata;
38 vector<SharedRAbundVector*> lookup;
39 vector<Calculator*> heatCalculators;
40 ValidCalculators* validCalculator;
43 map<string, string> parameters;
44 map<string, string>::iterator it;
46 set<string> labels; //holds labels to be used
47 string format, groups, label, calc, phylipfile, columnfile, namefile, outputDir;
48 vector<string> Estimators, Groups, outputNames;
49 map<string, vector<string> > outputTypes;
51 int runCommandShared();