X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.h;h=2b9e8e7f042e5f63a8805a427a8c3f8693f6cad9;hb=HEAD;hp=39795dc3055e1a1f8a057d3335b265c4d5ce4209;hpb=ee4dd201fa4f2c4ede5b2e525c82cce0a37de363;p=mothur.git

diff --git a/otuhierarchycommand.h b/otuhierarchycommand.h
index 39795dc..2b9e8e7 100644
--- a/otuhierarchycommand.h
+++ b/otuhierarchycommand.h
@@ -18,16 +18,31 @@ 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;
+	set<string> mylabels; //holds labels to be used
+	string label, listFile, outputDir, output, list1Label, list2Label;
+	vector<string> outputNames;
 	
-	vector<ListVector> getListVectors();
+	vector< vector<string> > getListVectors();
+    vector< vector<string> > getListVector(string, string&);
 		
 };