X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.h;h=a4ffea9c529829da3c3f08cfbc41c5e3bdf5ddcf;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=c590ec640dbbfec2f9cbc886041aadfe614fd719;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/removelineagecommand.h b/removelineagecommand.h
index c590ec6..a4ffea9 100644
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -19,17 +19,20 @@ 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"; }
+		string getDescription()		{ return "removes sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
+
+		int execute(); 
+		void help() { m->mothurOut(getHelpString()); }	
+	
 	private:
 		set<string> names;
-		vector<string> outputNames;
-		map<string, vector<string> > outputTypes;
+		vector<string> outputNames, listOfTaxons;
 		string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
 		bool abort, dups;
 		
@@ -39,7 +42,7 @@ class RemoveLineageCommand : public Command {
 		int readAlign();
 		int readList();
 		int readTax();	
-		string removeConfidences(string);
+		vector< map<string, float> > getTaxons(string);
 };
 
 #endif