changing command name classify.shared to classifyrf.shared

[mothur.git] / secondarystructurecommand.h

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index 110f019f3beeafdd2a877c423b250232a488e62c..ce97a2243c2b9da797e5a34da3454050b5002396 100644 (file)
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -39,8 +39,9 @@ class AlignCheckCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "align.check";                         }
                string getCommandCategory()             { return "Sequence Processing";         }
-               string getOutputFileNameTag(string, string);
+               
        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"; }
 
@@ -50,7 +51,7 @@ class AlignCheckCommand : public Command {
        
        private:
                vector<int> structMap;
-               string mapfile, fastafile, outputDir, namefile;
+               string mapfile, fastafile, outputDir, namefile, countfile;
                bool abort;
                int seqLength, haderror;
                vector<string> outputNames;