X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.h;h=cd106ece49d90dcfe28a0d272b672919281a912b;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=c6749ef3841800971f82f5a01c54d76de713b096;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/otuhierarchycommand.h b/otuhierarchycommand.h
index c6749ef..cd106ec 100644
--- a/otuhierarchycommand.h
+++ b/otuhierarchycommand.h
@@ -18,14 +18,28 @@ class OtuHierarchyCommand : public Command {
 
 public:
 	OtuHierarchyCommand(string);
-	~OtuHierarchyCommand();
-	int execute();
-	void help();
+	OtuHierarchyCommand();
+	~OtuHierarchyCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "otu.hierarchy";			}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Otu.hierarchy"; }
+	string getDescription()		{ return "relates OTUs at different distances"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
 	bool abort;
 	set<string> labels; //holds labels to be used
-	string label, listFile, outputDir;
+	string label, listFile, outputDir, output;
+	vector<string> outputNames;
 	
 	vector<ListVector> getListVectors();