X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.h;h=a756d24f583be82eac03634ebcd8496c4fd687b6;hb=cc19310422f125d6628980bd1148e1e816792382;hp=124f6e309f4b5e6a5842f88da7fdcaabbbf22eac;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/removelineagecommand.h b/removelineagecommand.h
index 124f6e3..a756d24 100644
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -23,25 +23,27 @@ 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;
-		string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+		vector<string> outputNames, listOfTaxons;
+		string fastafile, namefile, groupfile, alignfile, listfile, countfile, taxfile, outputDir, taxons;
 		bool abort, dups;
 		
 		int readFasta();
 		int readName();
 		int readGroup();
+        int readCount();
 		int readAlign();
 		int readList();
 		int readTax();	
-		string removeConfidences(string);
 		vector< map<string, float> > getTaxons(string);
 };