X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.h;h=2b9e8e7f042e5f63a8805a427a8c3f8693f6cad9;hb=1ef03d78c36b105e87165ad1ebc9af29cd6144b7;hp=8a2c862cb66398ec1c00e964c627d158fc0d39c0;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf;p=mothur.git

diff --git a/otuhierarchycommand.h b/otuhierarchycommand.h
index 8a2c862..2b9e8e7 100644
--- a/otuhierarchycommand.h
+++ b/otuhierarchycommand.h
@@ -24,7 +24,9 @@ public:
 	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"; }
 
@@ -35,11 +37,12 @@ public:
 	
 private:
 	bool abort;
-	set<string> labels; //holds labels to be used
-	string label, listFile, outputDir, output;
+	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&);
 		
 };