X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=hclustercommand.h;h=9241e94c35441e1b0d09d3bddae9a76d8f6c4cc6;hb=0e051b4cfda410b0d441da6ff2f96d4bbe1d9e5a;hp=443d8709bb7dd9294841e2dfc24584569e78e7c0;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/hclustercommand.h b/hclustercommand.h
index 443d870..9241e94 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 +31,20 @@
 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();	
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	GlobalData* globaldata;
 	HCluster* cluster;
 	ListVector* list;
 	RAbundVector* rabund;
@@ -46,13 +52,14 @@ 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;
 	ofstream sabundFile, rabundFile, listFile;
 	time_t start;
 	unsigned long loops;
+	vector<string> outputNames;
 	
 	void printData(string label);
 };