X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;h=110f019f3beeafdd2a877c423b250232a488e62c;hb=ccae9eef0b44f2d63fdf4a707d0d40243aa1b990;hp=2e04936a8eea682d1f8511de11a16a601c9e9d1c;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index 2e04936..110f019 100644
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -39,7 +39,11 @@ class AlignCheckCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "align.check";				}
 		string getCommandCategory()		{ return "Sequence Processing";		}
-		string getHelpString();	
+		string getOutputFileNameTag(string, string);
+	string getHelpString();	
+		string getCitation() { return "http://www.mothur.org/wiki/Align.check"; }
+		string getDescription()		{ return "calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment"; }
+
 	
 		int execute(); 
 		void help() { m->mothurOut(getHelpString()); }