working on pam

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 487c4601780a209418be72b8eb8c04edd0a55442..e514bdae70f7e0b51854b40baacf44d2b0174c8a 100644 (file)
--- 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. */ 
@@ -26,7 +27,9 @@ public:
        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"; }
 
@@ -36,7 +39,7 @@ public:
        
        
 private:
-       string inFastaName, oldNameMapFName, outputDir;
+       string inFastaName, oldNameMapFName, outputDir, countfile;
        vector<string> outputNames;
 
        bool abort;