working on pam

[mothur.git] / getlabelcommand.h

diff --git a/getlabelcommand.h b/getlabelcommand.h
index 00945e1b362e6e19cf705cf77ee16a15e5a3ccf0..26ec6550b4f6b7fb622b60c1b711fc24c0c4ac40 100644 (file)
--- a/getlabelcommand.h
+++ b/getlabelcommand.h
@@ -11,28 +11,33 @@
  */
 
 #include "command.hpp"
-#include "readmatrix.hpp"
+#include "ordervector.hpp"
+#include "inputdata.h"
 
-class GlobalData;
 
 class GetlabelCommand : public Command {
 public:
        GetlabelCommand(string);
-       GetlabelCommand(){}
-       ~GetlabelCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       GetlabelCommand();
+       ~GetlabelCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.label";                           }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+    string getOutputPattern(string) { return ""; }     
+       string getCitation() { return "http://www.mothur.org/wiki/Get.label"; }
+       string getDescription()         { return "outputs labels"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
-       string filename;
+       string inputfile, listfile, rabundfile, sabundfile, format;
        bool abort;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
 };
 
 #endif