1.21.0

[mothur.git] / removegroupscommand.h

diff --git a/removegroupscommand.h b/removegroupscommand.h
index 896697aa4cfe7c9cfa7532db6e94b5f5590050ad..63c0bff316ceda8770afdf19c90bb8f1feed7e6e 100644 (file)
--- a/removegroupscommand.h
+++ b/removegroupscommand.h
@@ -21,22 +21,27 @@ 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(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Remove.groups"; }
+       string getDescription()         { return "removes sequences from a list, fasta, name, group or taxonomy file from a given group or set of groups"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
        set<string> names;
-       string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+       string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups, sharedfile;
        bool abort;
        vector<string> outputNames, Groups;
-       map<string, vector<string> > outputTypes;
        GroupMap* groupMap;
        
        int readFasta();
+       int readShared();
        int readName();
        int readGroup();
        void readAccnos();