X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=hclustercommand.h;h=d1074070420fc89347a65b8fa8c0448c953c8881;hp=8bbc655fd7c30a9708b8292a81de0bb6a7b6c478;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0

diff --git a/hclustercommand.h b/hclustercommand.h
index 8bbc655..d107407 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"
@@ -32,13 +31,24 @@
 class HClusterCommand : public Command {
 	
 public:
-	HClusterCommand(string);	
-	~HClusterCommand();
-	int execute();	
-	void help();
+	HClusterCommand(string);
+	HClusterCommand();	
+	~HClusterCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "hcluster";	}
+	string getCommandCategory()		{ return "Clustering";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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;
@@ -46,7 +56,7 @@ private:
 	ListVector oldList;
 	ReadCluster* read;
 	
-	bool abort, sorted, print_start;
+	bool abort, sorted, print_start, hard;
 	string method, fileroot, tag, distfile, format, phylipfile, columnfile, namefile, sort, showabund, timing, outputDir;
 	double cutoff;
 	int precision, length;