X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapsimcommand.h;fp=heatmapsimcommand.h;h=74e20bebb35863128f72c3d85a8398c87ad9a5b2;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

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
+