X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=heatmapcommand.h;h=fc5165ed65b9aa63e56de900acafcede5cc4d43c;hp=5eeae265471785c8d582e7b250c76046554711e7;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=29351fe29c017d2225366418973ed0e000ce5293

diff --git a/heatmapcommand.h b/heatmapcommand.h
index 5eeae26..fc5165e 100644
--- a/heatmapcommand.h
+++ b/heatmapcommand.h
@@ -13,32 +13,45 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readmatrix.hpp"
 #include "sharedlistvector.h"
 #include "heatmap.h"
-
-
-class GlobalData;
+#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();	
+    string getOutputPattern(string);	
+	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:
-	GlobalData* globaldata;
-	ReadMatrix* read;
 	InputData* input;
-	SharedListVector* SharedList;
-	SharedOrderVector* order;
-	OrderVector* ordersingle;
+	RAbundVector* rabund;
+	vector<SharedRAbundVector*> lookup;
+	vector<SharedRAbundFloatVector*> lookupFloat;
 	HeatMap* heatmap;
-	string format;
-	
-	void setGroups();
+
+	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;
+
 
 };