X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=hclustercommand.h;h=6bf559ae6937f130679a5b601e939d7b79193acc;hb=01f8d2c7d982a6209211f5abbcf2a086fdf60d0a;hp=fc0333174a87b111a0cda756dc24ff4669202cc9;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/hclustercommand.h b/hclustercommand.h
index fc03331..6bf559a 100644
--- a/hclustercommand.h
+++ b/hclustercommand.h
@@ -11,7 +11,6 @@
  */
 
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "hcluster.h"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
@@ -34,16 +33,21 @@ class HClusterCommand : public Command {
 public:
 	HClusterCommand(string);
 	HClusterCommand();	
-	~HClusterCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();	
-	void help();
+	~HClusterCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "hcluster";	}
+	string getCommandCategory()		{ return "Clustering";	}
+	string getOutputFileNameTag(string, string);
+	string getHelpString();	
+	string getCitation() { return "Sun Y, Cai Y, Liu L, Yu F, Farrell ML, Mckendree W, Farmerie W (2009). ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res 37: e76. \nhttp://www.mothur.org/wiki/Hcluster"; }
+	string getDescription()		{ return "cluster your sequences into OTUs using a distance matrix"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	GlobalData* globaldata;
 	HCluster* cluster;
 	ListVector* list;
 	RAbundVector* rabund;
@@ -59,7 +63,6 @@ private:
 	time_t start;
 	unsigned long loops;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	
 	void printData(string label);
 };