X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listseqscommand.h;h=8e4cce3c932100ff1ab88d49b346ff87e7791a06;hb=e8e13c129ba8184ec5932a090773f353f3ae3406;hp=04d9e1da99ae079bd9b10d2ba3e30d5b0ba2f01c;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/listseqscommand.h b/listseqscommand.h
index 04d9e1d..8e4cce3 100644
--- a/listseqscommand.h
+++ b/listseqscommand.h
@@ -16,21 +16,34 @@ class ListSeqsCommand : public Command {
 	
 	public:
 	
-		ListSeqsCommand(string);	
-		~ListSeqsCommand(){};
-		int execute();
-		void help();	
-		
+		ListSeqsCommand(string);
+		ListSeqsCommand();	
+		~ListSeqsCommand(){}
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "list.seqs";				}
+		string getCommandCategory()		{ return "Sequence Processing";		}
+		string getOutputFileNameTag(string, string);
+	string getHelpString();	
+		string getCitation() { return "http://www.mothur.org/wiki/List.seqs"; }
+		string getDescription()		{ return "lists sequences from a list, fasta, name, group, alignreport or taxonomy file"; }
+
+		int execute(); 
+		void help() { m->mothurOut(getHelpString()); }	
+	
+	
 	private:
-		vector<string> names;
-		string fastafile, namefile, groupfile, alignfile, inputFileName, outputDir, listfile;
+		vector<string> names, outputNames;
+		string fastafile, namefile, groupfile, countfile, alignfile, inputFileName, outputDir, listfile, taxfile;
 		bool abort;
 		
-		void readFasta();
-		void readName();
-		void readGroup();
-		void readAlign();
-		void readList();
+		int readFasta();
+		int readName();
+		int readGroup();
+		int readAlign();
+		int readList();
+		int readTax();
+        int readCount();
 		
 };