working on pam

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 88b7a382d4c175a14c243d21e97a7580cba9c32d..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. */ 
@@ -22,17 +23,24 @@ 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 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;
-       map<string, vector<string> > outputTypes;
 
        bool abort;
 };