X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.h;h=b89a509c5f76971d9df9de9a3fd4e9113a70b816;hb=e150b0b0664caec517485ee6d69dcdade6dcae77;hp=647cb765f0e75781862d0fa74305d55573c85872;hpb=81276c241b984898f8d30ad123c00592ee6db7b8;p=mothur.git

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 647cb76..b89a509 100644
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -17,21 +17,33 @@ class RemoveSeqsCommand : public Command {
 	public:
 	
 		RemoveSeqsCommand(string);	
-		~RemoveSeqsCommand(){};
-		int execute();
-		void help();	
-		
+		RemoveSeqsCommand();
+		~RemoveSeqsCommand(){}
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "remove.seqs";				}
+		string getCommandCategory()		{ return "Sequence Processing";		}
+		string getHelpString();	
+		string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
+	
+		int execute(); 
+		void help() { m->mothurOut(getHelpString()); }	
+	
+	
 	private:
 		set<string> names;
-		string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, outputDir;
+		string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
 		bool abort, dups;
+		vector<string> outputNames;
 		
-		void readFasta();
-		void readName();
-		void readGroup();
-		void readAlign();
+		int readFasta();
+		int readName();
+		int readGroup();
+		int readAlign();
 		void readAccnos();
-		void readList();
+		int readList();
+		int readTax();
+		int readQual();
 		
 };