working on mgcluster count file change

[mothur.git] / secondarystructurecommand.h

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index 2e04936a8eea682d1f8511de11a16a601c9e9d1c..110f019f3beeafdd2a877c423b250232a488e62c 100644 (file)
--- 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()); }