X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapsimcommand.h;h=2c3a470761d719af0bff13bc4d194e5164bd42e0;hb=ea4f373c28543cd1002b0dd7dc6e55c526647d59;hp=838babdbe388b69b57d56f01fa3d1e508e18faae;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h
index 838babd..2c3a470 100644
--- a/heatmapsimcommand.h
+++ b/heatmapsimcommand.h
@@ -12,35 +12,40 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "validcalculator.h"
 #include "heatmapsim.h"
-
-class GlobalData;
+#include "nameassignment.hpp"
 
 class HeatMapSimCommand : public Command {
 
 public:
 	HeatMapSimCommand(string);
-	~HeatMapSimCommand();
-	int execute();
-	void help();
+	HeatMapSimCommand();
+	~HeatMapSimCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "heatmap.sim";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getOutputFileNameTag(string, string);
+	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:
-	GlobalData* globaldata;
-	ReadOTUFile* read;
 	InputData* input;
 	vector<SharedRAbundVector*> lookup;
 	vector<Calculator*> heatCalculators;
-	ValidCalculators* validCalculator;
 	HeatMapSim* heatmap;
 	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
 	bool abort, allLines;
 	set<string> labels; //holds labels to be used
-	string format, groups, label, calc, phylipfile, columnfile, namefile, outputDir;
-	vector<string> Estimators, Groups;
+	string format, groups, label, calc, sharedfile, phylipfile, columnfile, countfile, namefile, outputDir, inputfile;
+	vector<string> Estimators, Groups, outputNames;
+	int fontsize;
 	
 	int runCommandShared();
 	int runCommandDist();