removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 88b7a382d4c175a14c243d21e97a7580cba9c32d..8a1cb87cb87f62b9c5dc1a0c4073d13675fe105e 100644 (file)
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -22,17 +22,19 @@ 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(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
        string inFastaName, oldNameMapFName, outputDir;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
 
        bool abort;
 };