added command descriptions

[mothur.git] / secondarystructurecommand.h

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index daee85a37fd4e13df952ea363da36227dde85143..4e7bdea09cac0d1bd86d780eb92e499bbe9bfc69 100644 (file)
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -41,6 +41,8 @@ class AlignCheckCommand : public Command {
                string getCommandCategory()             { return "Sequence Processing";         }
                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()); }