working on pam

[mothur.git] / countgroupscommand.h

diff --git a/countgroupscommand.h b/countgroupscommand.h
index dd0e0a23eb3ccb9a5f4072aa9bb076228f2fb8b2..cd226a3da2c02107f4512acc126b067d195dfb8c 100644 (file)
--- a/countgroupscommand.h
+++ b/countgroupscommand.h
@@ -23,8 +23,8 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "count.groups";                        }
        string getCommandCategory()             { return "Sequence Processing";         }
-       string getOutputFileNameTag(string, string) { return ""; }
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Count.groups"; }
        string getDescription()         { return "counts the number of sequences in each group"; }
        
@@ -33,9 +33,10 @@ public:
        
        
 private:
-       string sharedfile, groupfile, outputDir, groups, accnosfile;
+       string sharedfile, groupfile, countfile, outputDir, groups, accnosfile;
        bool abort;
        vector<string> Groups;
+    vector<string> outputNames;
 };
 
 #endif