added code to check path for uchime and catchall executables

[mothur.git] / getgroupcommand.h

diff --git a/getgroupcommand.h b/getgroupcommand.h
index fb3e810666320ea2cd1c32d4b14b0c2cac08c995..a3e47e0204e36bfa54970c1d5c0e3ecb9398ab90 100644 (file)
--- a/getgroupcommand.h
+++ b/getgroupcommand.h
@@ -11,26 +11,29 @@
  */
 
 #include "command.hpp"
-#include "globaldata.hpp"
 
 class GetgroupCommand : public Command {
 public:
        GetgroupCommand(string);
        GetgroupCommand();
-       ~GetgroupCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~GetgroupCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.group";                           }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.group"; }
+       string getDescription()         { return "outputs group names"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
-       GroupMap* groupMap;
-       string outputFile, sharedfile;
+       
+       string outputFile, sharedfile, outputDir;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        ofstream out;
        ifstream in;
        bool abort;