X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listseqscommand.h;h=8e4cce3c932100ff1ab88d49b346ff87e7791a06;hb=e10c72304ee071c0c40e0218a06d89dc4731cbc2;hp=be53d750ac0691938e314c883d689715bc8d11c7;hpb=39a0a86958038d71083fad3a1a50c02ba9c2fc67;p=mothur.git

diff --git a/listseqscommand.h b/listseqscommand.h
index be53d75..8e4cce3 100644
--- a/listseqscommand.h
+++ b/listseqscommand.h
@@ -23,15 +23,18 @@ class ListSeqsCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "list.seqs";				}
 		string getCommandCategory()		{ return "Sequence Processing";		}
-		string getHelpString();	
-	
+		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, outputNames;
-		string fastafile, namefile, groupfile, alignfile, inputFileName, outputDir, listfile, taxfile;
+		string fastafile, namefile, groupfile, countfile, alignfile, inputFileName, outputDir, listfile, taxfile;
 		bool abort;
 		
 		int readFasta();
@@ -40,6 +43,7 @@ class ListSeqsCommand : public Command {
 		int readAlign();
 		int readList();
 		int readTax();
+        int readCount();
 		
 };