X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapcommand.h;fp=heatmapcommand.h;h=ccd5f4868e9061ed61e4a90ae042ae6bded4fa68;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/heatmapcommand.h b/heatmapcommand.h
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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();
+	~HeatMapCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "heatmap.bin";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	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:
+	InputData* input;
+	RAbundVector* rabund;
+	vector<SharedRAbundVector*> lookup;
+	vector<SharedRAbundFloatVector*> lookupFloat;
+	HeatMap* heatmap;
+
+	bool abort, allLines;
+	set<string> labels; //holds labels to be used
+	string format, groups, sorted, scale, label, outputDir, sharedfile, relabundfile, listfile, rabundfile, sabundfile, inputfile;
+	vector<string> Groups, outputNames;
+	int numOTU, fontSize;
+
+
+};
+
+#endif
+