working on pam

[mothur.git] / getotuscommand.h

diff --git a/getotuscommand.h b/getotuscommand.h
index 30f4f3cb0b18aedb2a28348f41f720e967ea1d01..c71ab062b431c9ca7945c8e0b8679980058939c8 100644 (file)
--- a/getotuscommand.h
+++ b/getotuscommand.h
@@ -27,8 +27,12 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "get.otus";                            }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Get.otus"; }
+       string getDescription()         { return "outputs a new list file containing the otus containing sequences from the groups specified"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
@@ -40,7 +44,6 @@ private:
        vector<string> outputNames, Groups;
        GroupMap* groupMap;
        
-       void readAccnos();
        int readListGroup();
        int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);