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[mothur.git] / heatmapsimcommand.h

diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h
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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();
+       ~HeatMapSimCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "heatmap.sim";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       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:
+       InputData* input;
+       vector<SharedRAbundVector*> lookup;
+       vector<Calculator*> heatCalculators;
+       HeatMapSim* heatmap;
+       OptionParser* parser;
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string format, groups, label, calc, sharedfile, phylipfile, columnfile, namefile, outputDir, inputfile;
+       vector<string> Estimators, Groups, outputNames;
+       int fontsize;
+       
+       int runCommandShared();
+       int runCommandDist();
+
+
+};
+
+#endif
+