X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deuniqueseqscommand.h;h=5310b83b3002c8b3d52b32bdb56bf8cc772eddd2;hb=ce8794490ab1d83adcdb2b92e0302a1e43e17adf;hp=13176a80a413a1bce9d84bb4cf496702a554c446;hpb=f09bacac01a842a74c1c1b69070852cc969ff506;p=mothur.git

diff --git a/deuniqueseqscommand.h b/deuniqueseqscommand.h
index 13176a8..5310b83 100644
--- a/deuniqueseqscommand.h
+++ b/deuniqueseqscommand.h
@@ -19,18 +19,24 @@ public:
 	DeUniqueSeqsCommand(string);
 	DeUniqueSeqsCommand();
 	~DeUniqueSeqsCommand() {}
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();	
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "deunique.seqs";		}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getOutputFileNameTag(string, string);
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Deunique.seqs"; }
+	string getDescription()		{ return "reverse of the unique.seqs command, and creates a fasta file from a fasta and name file"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
 
 	string fastaFile, nameFile, outputDir;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	bool abort;
 	
 	map<string, string> nameMap;