X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=deconvolutecommand.h;h=e514bdae70f7e0b51854b40baacf44d2b0174c8a;hp=9c8fd22d702f8a8b98ee12d682d6f880e5c1fb0e;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 9c8fd22..e514bda 100644
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -11,6 +11,7 @@
 
 #include "command.hpp"
 #include "fastamap.h"
+#include "counttable.h"
 
 /* The unique.seqs command reads a fasta file, finds the duplicate sequences and outputs a names file
 	containing 2 columns.  The first being the groupname and the second the list of identical sequence names. */ 
@@ -20,12 +21,26 @@ class DeconvoluteCommand : public Command {
 
 public:
 	DeconvoluteCommand(string);
-	~DeconvoluteCommand() { };
-	int execute();
-	void help();	
+	DeconvoluteCommand();
+	~DeconvoluteCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "unique.seqs";		}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+    
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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;
+	string inFastaName, oldNameMapFName, outputDir, countfile;
+	vector<string> outputNames;
 
 	bool abort;
 };