X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.h;h=ad6da0cf529121202b3bfc5d1c1d6bdc166cba16;hb=5c5c0428f6d548c28a8b903ac80efed4f92d59db;hp=39795dc3055e1a1f8a057d3335b265c4d5ce4209;hpb=ee4dd201fa4f2c4ede5b2e525c82cce0a37de363;p=mothur.git

diff --git a/otuhierarchycommand.h b/otuhierarchycommand.h
index 39795dc..ad6da0c 100644
--- a/otuhierarchycommand.h
+++ b/otuhierarchycommand.h
@@ -18,14 +18,27 @@ 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 getOutputFileNameTag(string, string);
+	string getHelpString();	
+	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;
+	string label, listFile, outputDir, output;
+	vector<string> outputNames;
 	
 	vector<ListVector> getListVectors();