X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapcommand.h;h=a85d510074c55a73adc25b07f16a8a81bdd4a30c;hb=cdf9083dc32543cc640e72e9ca3aee0323cbad45;hp=f75c06425e7b6af1232809fb8a2f1f98c20d98aa;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git

diff --git a/heatmapcommand.h b/heatmapcommand.h
index f75c064..a85d510 100644
--- a/heatmapcommand.h
+++ b/heatmapcommand.h
@@ -13,32 +13,43 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "sharedlistvector.h"
 #include "heatmap.h"
-#include "sharedutilities.h"
-
+#include "rabundvector.hpp"
 
 class GlobalData;
 
-
 class HeatMapCommand : public Command {
 
 public:
+	HeatMapCommand(string);
 	HeatMapCommand();
 	~HeatMapCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();
+	void help();
 	
 private:
 	GlobalData* globaldata;
-	ReadMatrix* read;
-	SharedUtil* util;
+	ReadOTUFile* read;
 	InputData* input;
 	SharedListVector* SharedList;
-	SharedOrderVector* order;
-	OrderVector* ordersingle;
+	RAbundVector* rabund;
+	vector<SharedRAbundVector*> lookup;
+	vector<SharedRAbundFloatVector*> lookupFloat;
 	HeatMap* heatmap;
-	string format;
+
+	bool abort, allLines;
+	set<string> labels; //holds labels to be used
+	string format, groups, sorted, scale, label, outputDir;
+	vector<string> Groups, outputNames;
+	map<string, vector<string> > outputTypes;
+	int numOTU, fontSize;
+
 
 };