X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=reversecommand.h;h=2c7a9e4ee025e3ce8e94f328eb2cb1e676611cf6;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=2a996e9fe02d6e05511ea543ef0d9dd4e507fbdb;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/reversecommand.h b/reversecommand.h
index 2a996e9..2c7a9e4 100644
--- a/reversecommand.h
+++ b/reversecommand.h
@@ -10,25 +10,31 @@
  *
  */
 
-#include "mothur.h"
 #include "command.hpp"
-#include "globaldata.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:
-	GlobalData* globaldata;	
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
-	bool abort;
-	string fasta;
 
+	bool abort;
+	string fastaFileName, qualFileName, outputDir;
+	vector<string> outputNames;
 	
 };