changing command name classify.shared to classifyrf.shared

[mothur.git] / setcurrentcommand.h

diff --git a/setcurrentcommand.h b/setcurrentcommand.h
index 98033b7b8d8bb4f1e68c5b62df4ddd97e239a35e..effc266fc0dfaccd13d5d1e1fdbe6c348d4428d6 100644 (file)
--- a/setcurrentcommand.h
+++ b/setcurrentcommand.h
@@ -18,25 +18,30 @@ class SetCurrentCommand : public Command {
 public:
        SetCurrentCommand(string);
        SetCurrentCommand();
-       ~SetCurrentCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~SetCurrentCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "set.current"; }
+       string getCommandCategory()             { return "General";             }
+       
+       string getHelpString(); 
+    string getOutputPattern(string){ return ""; }      
+       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()); }  
        
 private:
        
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        bool abort;
        
        string clearTypes;
        vector<string> types;
        
-       string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
-       string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile;
+       string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile, summaryfile;
+       string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 
        
 };