X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=deconvolutecommand.h;h=673ffc9e4d2e689cd32c6b16867089fe43f216d1;hb=16f9c4ab6f39769856b13e048eae2c8eaa413c02;hp=4cb6aac3e0c9cd23d7b1d11ed40b775d43d4d42d;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 4cb6aac..673ffc9 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. */ 
@@ -19,13 +20,26 @@
 class DeconvoluteCommand : public Command {
 
 public:
-	DeconvoluteCommand(string);	
-	~DeconvoluteCommand() { };
-	int execute();
-	void help();	
+	DeconvoluteCommand(string);
+	DeconvoluteCommand();
+	~DeconvoluteCommand() {}
+	
+	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;
+	string inFastaName, oldNameMapFName, outputDir, countfile;
+	vector<string> outputNames;
 
 	bool abort;
 };