X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listseqscommand.h;h=1a31a6dd432e837159be8d916f7ce2a25e4d4dec;hb=8e67e9de1b200106bea5a468ac02125954656499;hp=4e0febd9c6dc84a7b49589e614c076493638c913;hpb=861f46b74c17adec8c6ad6d89f232ae7485797bf;p=mothur.git

diff --git a/listseqscommand.h b/listseqscommand.h
index 4e0febd..1a31a6d 100644
--- a/listseqscommand.h
+++ b/listseqscommand.h
@@ -16,20 +16,33 @@ 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;
+		vector<string> names, outputNames;
+		string fastafile, namefile, groupfile, alignfile, inputFileName, outputDir, listfile, taxfile;
 		bool abort;
 		
-		void readFasta();
-		void readName();
-		void readGroup();
-		void readAlign();
+		int readFasta();
+		int readName();
+		int readGroup();
+		int readAlign();
+		int readList();
+		int readTax();
 		
 };