modified reverse.seqs and qualscores.cpp

[mothur.git] / reversecommand.h

diff --git a/reversecommand.h b/reversecommand.h
index 46211a5e008d9194d8c18cdaed0bbeed04afb4e5..bd8d1194ff095fa5fecff1b51570520b849dbf9a 100644 (file)
--- a/reversecommand.h
+++ b/reversecommand.h
@@ -10,18 +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; 
+
+       bool abort;
+       string fastaFileName, qualFileName, outputDir;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
 };