X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.h;h=124f6e309f4b5e6a5842f88da7fdcaabbbf22eac;hb=e150b0b0664caec517485ee6d69dcdade6dcae77;hp=02a4440e79ec4a7e996b58a7b9209b30cc933dcd;hpb=a4f05f09c250323132a4b9427f41a3ededaec634;p=mothur.git

diff --git a/removelineagecommand.h b/removelineagecommand.h
index 02a4440..124f6e3 100644
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -19,17 +19,19 @@ class RemoveLineageCommand : public Command {
 		RemoveLineageCommand(string);
 		RemoveLineageCommand();
 		~RemoveLineageCommand(){};
-		vector<string> getRequiredParameters();
-		vector<string> getValidParameters();
-		vector<string> getRequiredFiles();
-		map<string, vector<string> > getOutputFiles() { return outputTypes; }
-		int execute();
-		void help();	
-		
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "remove.lineage";			}
+		string getCommandCategory()		{ return "Phylotype Analysis";		}
+		string getHelpString();	
+		string getCitation() { return "http://www.mothur.org/wiki/Remove.lineage"; }
+	
+		int execute(); 
+		void help() { m->mothurOut(getHelpString()); }	
+	
 	private:
 		set<string> names;
 		vector<string> outputNames;
-		map<string, vector<string> > outputTypes;
 		string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
 		bool abort, dups;