sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / getotuscommand.h

diff --git a/getotuscommand.h b/getotuscommand.h
index ec69acb4c0381c6b2b5190abf1a88ae214751647..c71ab062b431c9ca7945c8e0b8679980058939c8 100644 (file)
--- a/getotuscommand.h
+++ b/getotuscommand.h
@@ -23,21 +23,27 @@ public:
        GetOtusCommand(string); 
        GetOtusCommand();
        ~GetOtusCommand(){}
-       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 "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()); }  
+       
        
 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&);