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

[mothur.git] / removegroupscommand.h

diff --git a/removegroupscommand.h b/removegroupscommand.h
index 896697aa4cfe7c9cfa7532db6e94b5f5590050ad..955d94d5090b5fc6caf4ba2a937261a173a3eb91 100644 (file)
--- a/removegroupscommand.h
+++ b/removegroupscommand.h
@@ -21,19 +21,21 @@ public:
        RemoveGroupsCommand(string);    
        RemoveGroupsCommand();
        ~RemoveGroupsCommand(){}
-       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.groups";                       }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
        set<string> names;
        string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
        bool abort;
        vector<string> outputNames, Groups;
-       map<string, vector<string> > outputTypes;
        GroupMap* groupMap;
        
        int readFasta();