X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.h;h=de1e3d9d6aff8595a098cf8bf2fd6c1d5c79ec9f;hb=6973be461c47c057531f447de22003a30cabc193;hp=1dcb0fceab5ed3800d2b604d2ba32ff632cfec8c;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 1dcb0fc..de1e3d9 100644
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -17,21 +17,30 @@ class RemoveSeqsCommand : public Command {
 	public:
 	
 		RemoveSeqsCommand(string);	
-		~RemoveSeqsCommand(){};
+		RemoveSeqsCommand();
+		~RemoveSeqsCommand(){}
+		vector<string> getRequiredParameters();
+		vector<string> getValidParameters();
+		vector<string> getRequiredFiles();
+		map<string, vector<string> > getOutputFiles() { return outputTypes; }
 		int execute();
 		void help();	
 		
 	private:
 		set<string> names;
-		string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, outputDir;
-		bool abort;
+		string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+		bool abort, dups;
+		vector<string> outputNames;
+		map<string, vector<string> > outputTypes;
 		
-		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();
 		
 };