X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.h;h=b249072e41aba8b7ff0501c1fc946b90c48dfd22;hb=fd5f17bcbe5fadab2c525f3d1fcfd1d79a60ae72;hp=809109c486de9f00b39091b863da8a23dfc95a96;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/getseqscommand.h b/getseqscommand.h
index 809109c..b249072 100644
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -17,22 +17,30 @@ class GetSeqsCommand : public Command {
 	public:
 	
 		GetSeqsCommand(string);
+		GetSeqsCommand();
 		~GetSeqsCommand(){};
+		vector<string> getRequiredParameters();
+		vector<string> getValidParameters();
+		vector<string> getRequiredFiles();
+		map<string, vector<string> > getOutputFiles() { return outputTypes; }
 		int execute();
 		void help();	
 		
 	private:
 		set<string> names;
 		vector<string> outputNames;
-		string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, outputDir;
-		bool abort;
+		string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+		bool abort, dups;
+		map<string, vector<string> > outputTypes;
 		
-		void readFasta();
-		void readName();
-		void readGroup();
-		void readAlign();
-		void readAccnos();
-		void readList();
+		int readFasta();
+		int readName();
+		int readGroup();
+		int readAlign();
+		int readAccnos();
+		int readList();
+		int readTax();
+		int readQual();
 		
 };