added pipeline commands which involved change to command factory and command class...

[mothur.git] / reversecommand.h

diff --git a/reversecommand.h b/reversecommand.h
index 2a996e9fe02d6e05511ea543ef0d9dd4e507fbdb..8b5bcd262528e36f756093a8236f8a1b3a447ce8 100644 (file)
--- a/reversecommand.h
+++ b/reversecommand.h
@@ -10,25 +10,26 @@
  *
  */
 
-#include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
 
 class ReverseSeqsCommand : public Command {
 public:
        ReverseSeqsCommand(string);
+       ReverseSeqsCommand();
        ~ReverseSeqsCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
 private:
-       GlobalData* globaldata; 
-       OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it;
-       bool abort;
-       string fasta;
 
+       bool abort;
+       string fasta, outputDir;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
 };