working on pam

[mothur.git] / secondarystructurecommand.h

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index daee85a37fd4e13df952ea363da36227dde85143..ce97a2243c2b9da797e5a34da3454050b5002396 100644 (file)
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -39,15 +39,19 @@ class AlignCheckCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "align.check";                         }
                string getCommandCategory()             { return "Sequence Processing";         }
-               string getHelpString(); 
+               
+       string getHelpString(); 
+    string getOutputPattern(string);   
                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()); }  
        
        private:
                vector<int> structMap;
-               string mapfile, fastafile, outputDir, namefile;
+               string mapfile, fastafile, outputDir, namefile, countfile;
                bool abort;
                int seqLength, haderror;
                vector<string> outputNames;