X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.h;h=474951a9feaee7d497417cf2a03f206367056241;hb=44f3a3c81a34fdee62550d98838a4b421e8df08e;hp=1f429d92810402f64a1c2d776510719aa7113610;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 1f429d9..474951a 100644
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -17,13 +17,24 @@ 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 getOutputFileNameTag(string, string);
+	string getHelpString();	
+		string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
+		string getDescription()		{ return "removes sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
+		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;
 		
@@ -31,8 +42,9 @@ class RemoveSeqsCommand : public Command {
 		int readName();
 		int readGroup();
 		int readAlign();
-		void readAccnos();
 		int readList();
+		int readTax();
+		int readQual();
 		
 };