optimizing classify.seqs calculating of template probabilities.

[mothur.git] / reversecommand.h

diff --git a/reversecommand.h b/reversecommand.h
index aad454313b6668699ea8626cfdf883b8b2d4902e..2c7a9e4ee025e3ce8e94f328eb2cb1e676611cf6 100644 (file)
--- a/reversecommand.h
+++ b/reversecommand.h
@@ -10,20 +10,31 @@
  *
  */
 
-#include "mothur.h"
 #include "command.hpp"
 
 class ReverseSeqsCommand : public Command {
 public:
        ReverseSeqsCommand(string);
-       ~ReverseSeqsCommand();
-       int execute();
-       void help();
+       ReverseSeqsCommand();
+       ~ReverseSeqsCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "reverse.seqs";                        }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getOutputFileNameTag(string, string);
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Reverse.seqs"; }
+       string getDescription()         { return "outputs a fasta file containing the reverse-complements"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
 
        bool abort;
-       string fasta, outputDir;
+       string fastaFileName, qualFileName, outputDir;
+       vector<string> outputNames;
        
 };