X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=otuhierarchycommand.h;h=cd106ece49d90dcfe28a0d272b672919281a912b;hp=dd5f3a7adc759733bf3972392485c79b94669977;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/otuhierarchycommand.h b/otuhierarchycommand.h
index dd5f3a7..cd106ec 100644
--- a/otuhierarchycommand.h
+++ b/otuhierarchycommand.h
@@ -19,20 +19,27 @@ class OtuHierarchyCommand : public Command {
 public:
 	OtuHierarchyCommand(string);
 	OtuHierarchyCommand();
-	~OtuHierarchyCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~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, output;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	
 	vector<ListVector> getListVectors();