X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=reversecommand.h;h=f7f729c9848ae0fa972944ae5b51ec18cceaca1d;hp=8b5bcd262528e36f756093a8236f8a1b3a447ce8;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/reversecommand.h b/reversecommand.h
index 8b5bcd2..f7f729c 100644
--- a/reversecommand.h
+++ b/reversecommand.h
@@ -16,20 +16,26 @@ 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();
+	~ReverseSeqsCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "reverse.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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;
-	map<string, vector<string> > outputTypes;
 	
 };