added count file to get.groups and remove.groups. added shortcut parameter to classif...

[mothur.git] / setcurrentcommand.h

diff --git a/setcurrentcommand.h b/setcurrentcommand.h
index e942e60b436acbd5ad9a014ddc8176c899e14806..e741399844347f3db0a936cd2581ce9ba45dd7b2 100644 (file)
--- a/setcurrentcommand.h
+++ b/setcurrentcommand.h
@@ -23,9 +23,11 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "set.current"; }
        string getCommandCategory()             { return "General";             }
+       string getOutputFileNameTag(string, string) { return ""; }
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Set.current"; }
-       
+       string getDescription()         { return "set current files for mothur"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
@@ -37,7 +39,7 @@ private:
        string clearTypes;
        vector<string> types;
        
-       string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
+       string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile;
        string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;