X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=heatmapcommand.h;h=fc5165ed65b9aa63e56de900acafcede5cc4d43c;hp=a85d510074c55a73adc25b07f16a8a81bdd4a30c;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/heatmapcommand.h b/heatmapcommand.h
index a85d510..fc5165e 100644
--- a/heatmapcommand.h
+++ b/heatmapcommand.h
@@ -13,31 +13,34 @@
 
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sharedlistvector.h"
 #include "heatmap.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();
+	~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;
-	ReadOTUFile* read;
 	InputData* input;
-	SharedListVector* SharedList;
 	RAbundVector* rabund;
 	vector<SharedRAbundVector*> lookup;
 	vector<SharedRAbundFloatVector*> lookupFloat;
@@ -45,9 +48,8 @@ private:
 
 	bool abort, allLines;
 	set<string> labels; //holds labels to be used
-	string format, groups, sorted, scale, label, outputDir;
+	string format, groups, sorted, scale, label, outputDir, sharedfile, relabundfile, listfile, rabundfile, sabundfile, inputfile;
 	vector<string> Groups, outputNames;
-	map<string, vector<string> > outputTypes;
 	int numOTU, fontSize;