X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.h;h=124f6e309f4b5e6a5842f88da7fdcaabbbf22eac;hb=1c898913f53fe4c6574102896b967d9347d1b42a;hp=60712c95e8455e020e9fc77a0a851d41c36f06c4;hpb=8f89a92f4ada82a2b3bf51b23b6a977770f2b9e2;p=mothur.git

diff --git a/removelineagecommand.h b/removelineagecommand.h
index 60712c9..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;
 		
@@ -40,7 +42,7 @@ class RemoveLineageCommand : public Command {
 		int readList();
 		int readTax();	
 		string removeConfidences(string);
-		vector< map<string, int> > getTaxons(string);
+		vector< map<string, float> > getTaxons(string);
 };
 
 #endif