X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;h=110f019f3beeafdd2a877c423b250232a488e62c;hb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;hp=daee85a37fd4e13df952ea363da36227dde85143;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index daee85a..110f019 100644
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -39,8 +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()); }