X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=deconvolutecommand.h;h=e514bdae70f7e0b51854b40baacf44d2b0174c8a;hp=7d4cb50023eb6312b652a8368d2d862882b3ffd4;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=f687723a8357916e86a05116978e6869b039ce36

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 7d4cb50..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. */ 
@@ -26,8 +27,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "unique.seqs";		}
 	string getCommandCategory()		{ return "Sequence Processing";		}
-    string getOutputFileNameTag(string, string);
+    
 	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"; }
 
@@ -37,7 +39,7 @@ public:
 	
 	
 private:
-	string inFastaName, oldNameMapFName, outputDir;
+	string inFastaName, oldNameMapFName, outputDir, countfile;
 	vector<string> outputNames;
 
 	bool abort;