X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=heatmapsimcommand.h;h=dbaa6840b4513ca085da696c485e5b73e74f37b9;hb=65f2be9d8f9b4cf72b4aafd800fdd11ad26435fd;hp=33696a33ac87b34bedea636810b32e4daa09be8c;hpb=f15f7092c97277337d4fdd9ef674015c15a13220;p=mothur.git

diff --git a/heatmapsimcommand.h b/heatmapsimcommand.h
index 33696a3..dbaa684 100644
--- a/heatmapsimcommand.h
+++ b/heatmapsimcommand.h
@@ -12,27 +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();
-	~HeatMapSimCommand();
-	int execute();
+	~HeatMapSimCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "heatmap.sim";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	
+	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;
+	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 runCommandShared();
+	int runCommandDist();
+
 
 };