X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.h;h=7d4cb50023eb6312b652a8368d2d862882b3ffd4;hb=6ede3bf5c0a9eedb23f24577a97da81ab3e1f7df;hp=88b7a382d4c175a14c243d21e97a7580cba9c32d;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 88b7a38..7d4cb50 100644
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -22,17 +22,23 @@ public:
 	DeconvoluteCommand(string);
 	DeconvoluteCommand();
 	~DeconvoluteCommand() {}
-	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 "unique.seqs";		}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+    string getOutputFileNameTag(string, string);
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Unique.seqs"; }
+	string getDescription()		{ return "creates a fasta containing the unique sequences as well as a namesfile with the names each sequence represents"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
 	string inFastaName, oldNameMapFName, outputDir;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 
 	bool abort;
 };