X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.h;h=9fdca48db66da3e0ddf5c603949c7380e61155b0;hb=1cf188b912d6da8f2cd03dd71cecef664a699c1a;hp=c590ec640dbbfec2f9cbc886041aadfe614fd719;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/removelineagecommand.h b/removelineagecommand.h
index c590ec6..9fdca48 100644
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -19,17 +19,18 @@ 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();	
+	
+		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;
 		
@@ -40,6 +41,7 @@ class RemoveLineageCommand : public Command {
 		int readList();
 		int readTax();	
 		string removeConfidences(string);
+		vector< map<string, float> > getTaxons(string);
 };
 
 #endif