X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=deuniqueseqscommand.h;h=042ff498fce19a60cd51d7b1393ec2cd4074123c;hp=13176a80a413a1bce9d84bb4cf496702a554c446;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=f09bacac01a842a74c1c1b69070852cc969ff506

diff --git a/deuniqueseqscommand.h b/deuniqueseqscommand.h
index 13176a8..042ff49 100644
--- a/deuniqueseqscommand.h
+++ b/deuniqueseqscommand.h
@@ -19,23 +19,27 @@ 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 getHelpString();	
+    string getOutputPattern(string);	
+	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;
+	string fastaFile, nameFile, outputDir, countfile;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	bool abort;
-	
-	map<string, string> nameMap;
-	
-	int readNamesFile();
+
 	
 };