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#ifndef HEATMAPSIMCOMMAND_H
#define HEATMAPSIMCOMMAND_H
/*
* heatmapsimcommand.h
* Mothur
*
* Created by Sarah Westcott on 6/8/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "inputdata.h"
#include "validcalculator.h"
#include "heatmapsim.h"
#include "nameassignment.hpp"
class HeatMapSimCommand : public Command {
public:
HeatMapSimCommand(string);
~HeatMapSimCommand(){}
vector<string> setParameters();
string getCommandName() { return "heatmap.sim"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Heatmap.sim"; }
string getDescription() { return "generate a heatmap indicating the pairwise distance between multiple samples using a variety of calculators"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<Calculator*> heatCalculators;
HeatMapSim* heatmap;
bool abort, allLines;
set<string> labels; //holds labels to be used
string format, groups, label, calc, sharedfile, phylipfile, columnfile, countfile, namefile, inputfile;
vector<string> Estimators, Groups, outputNames;
int fontsize;
int runCommandShared();
int runCommandDist();
};
#endif
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