X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.h;h=aef789aa7dd80a656a66c3061a2e8cadd1fe081b;hb=4116449310d17a847470b84728cdefee5197e67e;hp=47f56f75c52f6ec3bf11128fa06ea14295571649;hpb=b9456b1087ade74251792e039f4e5021dbf32349;p=mothur.git

diff --git a/getseqscommand.h b/getseqscommand.h
index 47f56f7..aef789a 100644
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -6,7 +6,7 @@
  *  Mothur
  *
  *  Created by Sarah Westcott on 7/8/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
  
@@ -16,21 +16,32 @@ class GetSeqsCommand : public Command {
 	
 	public:
 	
-		GetSeqsCommand(string);	
+		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;
-		string accnosfile, fastafile, namefile, groupfile, alignfile;
-		bool abort;
+		vector<string> outputNames;
+		string accnosfile, accnosfile2, 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();
+		int readFasta();
+		int readName();
+		int readGroup();
+		int readAlign();
+		int readAccnos();
+		int readList();
+		int readTax();
+		int readQual();
+		int compareAccnos();
 		
 };