X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.h;h=a5caec8e4c3e0f04ec7744489c3f27c0a495e38d;hb=8e67e9de1b200106bea5a468ac02125954656499;hp=9fdca48db66da3e0ddf5c603949c7380e61155b0;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/removelineagecommand.h b/removelineagecommand.h
index 9fdca48..a5caec8 100644
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -23,14 +23,17 @@ class RemoveLineageCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "remove.lineage";			}
 		string getCommandCategory()		{ return "Phylotype Analysis";		}
-		string getHelpString();	
-	
+		string getOutputFileNameTag(string, string);
+	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;
+		vector<string> outputNames, listOfTaxons;
 		string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
 		bool abort, dups;
 		
@@ -40,7 +43,6 @@ class RemoveLineageCommand : public Command {
 		int readAlign();
 		int readList();
 		int readTax();	
-		string removeConfidences(string);
 		vector< map<string, float> > getTaxons(string);
 };