X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listseqscommand.h;h=9d320d9e9a94ad031826bc547d42a03b30e8ec30;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=bd7beae73360da9453911e7d5b755135a00f4d54;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/listseqscommand.h b/listseqscommand.h
index bd7beae..9d320d9 100644
--- a/listseqscommand.h
+++ b/listseqscommand.h
@@ -21,17 +21,21 @@ class ListSeqsCommand : public Command {
 		~ListSeqsCommand(){}
 	
 		vector<string> setParameters();
-		string getCommandName()			{ return "get.seqs";				}
+		string getCommandName()			{ return "list.seqs";				}
 		string getCommandCategory()		{ return "Sequence Processing";		}
-		string getHelpString();	
-	
+		
+	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, outputNames;
-		string fastafile, namefile, groupfile, alignfile, inputFileName, outputDir, listfile, taxfile;
+		string fastafile, namefile, groupfile, countfile, alignfile, inputFileName, outputDir, listfile, taxfile, fastqfile;
 		bool abort;
 		
 		int readFasta();
@@ -40,7 +44,8 @@ class ListSeqsCommand : public Command {
 		int readAlign();
 		int readList();
 		int readTax();
-		
+        int readCount();
+        int readFastq();
 };
 
 #endif