added sff.multiple command. fixed issue with windows paralellization in chimera...

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 88b7a382d4c175a14c243d21e97a7580cba9c32d..7d4cb50023eb6312b652a8368d2d862882b3ffd4 100644 (file)
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -22,17 +22,23 @@ 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 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;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
 
        bool abort;
 };