X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapcommand.h;h=6fb5ff073fb5dea3b2a7237c114142ec0f3b184b;hb=836150c0a3666899ad58426388f4999d6cf8829a;hp=1b3c108836665085d953dc56b9aab20ae0687071;hpb=485c02be0cdcd06ce08dd58d551a525b6a1b47c5;p=mothur.git

diff --git a/heatmapcommand.h b/heatmapcommand.h
index 1b3c108..6fb5ff0 100644
--- a/heatmapcommand.h
+++ b/heatmapcommand.h
@@ -13,28 +13,40 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readmatrix.hpp"
 #include "sharedlistvector.h"
-
-
-class GlobalData;
+#include "heatmap.h"
+#include "rabundvector.hpp"
 
 
 class HeatMapCommand : public Command {
 
 public:
+	HeatMapCommand(string);
 	HeatMapCommand();
-	~HeatMapCommand();
-	int execute();
+	~HeatMapCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "heatmap.bin";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	string getHelpString();	
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	GlobalData* globaldata;
-	ReadMatrix* read;
 	InputData* input;
-	SharedListVector* SharedList;
-	SharedOrderVector* order;
-	OrderVector* ordersingle;
-	string format;
+	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;
+
 
 };