X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=listseqscommand.h;h=9d320d9e9a94ad031826bc547d42a03b30e8ec30;hp=04d9e1da99ae079bd9b10d2ba3e30d5b0ba2f01c;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=315e38cf393c82be238da5b32574f225a020d25c

diff --git a/listseqscommand.h b/listseqscommand.h
index 04d9e1d..9d320d9 100644
--- a/listseqscommand.h
+++ b/listseqscommand.h
@@ -16,22 +16,36 @@ 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 getHelpString();	
+    string getOutputPattern(string);	
+		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, fastqfile;
 		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();
+        int readFastq();
 };
 
 #endif