removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / removeotuscommand.h

diff --git a/removeotuscommand.h b/removeotuscommand.h
index 872b2c8caf1e7b082a040b2da15960f39dcb27e0..801eedc6b598820dc101ad73d505e43b87f8f926 100644 (file)
--- a/removeotuscommand.h
+++ b/removeotuscommand.h
@@ -21,18 +21,19 @@ public:
        RemoveOtusCommand(string);      
        RemoveOtusCommand();
        ~RemoveOtusCommand(){}
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();    
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "remove.otus";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        string accnosfile, groupfile, listfile, outputDir, groups, label;
        bool abort;
        vector<string> outputNames, Groups;
-       map<string, vector<string> > outputTypes;
        GroupMap* groupMap;
        
        void readAccnos();