changes while testing

[mothur.git] / removeotuscommand.h

diff --git a/removeotuscommand.h b/removeotuscommand.h
index ce1646b649e0ed34894b4bce5fd796421ccbc2f3..a7fcf0eaa1316203f0ec65c79094a2ef6f809ac3 100644 (file)
--- a/removeotuscommand.h
+++ b/removeotuscommand.h
@@ -10,8 +10,6 @@
  *
  */
 
-
-
 #include "command.hpp"
 #include "groupmap.h"
 #include "listvector.hpp"
@@ -23,21 +21,25 @@ 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(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Remove.otus"; }
+       string getDescription()         { return "outputs a new list file containing the otus NOT containing sequences from the groups specified"; }
+
+       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();
        int readListGroup();
        int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);