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#ifndef HEATMAPCOMMAND_H
#define HEATMAPCOMMAND_H
/*
* heatmapcommand.h
* Mothur
*
* Created by Sarah Westcott on 3/25/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "inputdata.h"
#include "sharedlistvector.h"
#include "heatmap.h"
#include "rabundvector.hpp"
class HeatMapCommand : public Command {
public:
HeatMapCommand(string);
~HeatMapCommand(){}
vector<string> setParameters();
string getCommandName() { return "heatmap.bin"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Heatmap.bin"; }
string getDescription() { return "generate a heatmap where the color represents the relative abundanceof an OTU"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, allLines;
set<string> labels; //holds labels to be used
string format, groups, sorted, scale, label, sharedfile, relabundfile, listfile, rabundfile, sabundfile, inputfile;
vector<string> Groups, outputNames;
int numOTU, fontSize;
};
#endif
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