added pipeline commands which involved change to command factory and command class...

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 635e53fe455ab05eacdb2a19e09837b30ef4c955..88b7a382d4c175a14c243d21e97a7580cba9c32d 100644 (file)
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -19,13 +19,20 @@
 class DeconvoluteCommand : public Command {
 
 public:
-       DeconvoluteCommand(string);     
-       ~DeconvoluteCommand() { };
+       DeconvoluteCommand(string);
+       DeconvoluteCommand();
+       ~DeconvoluteCommand() {}
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();    
        
 private:
-       string inFastaName, oldNameMapFName;
+       string inFastaName, oldNameMapFName, outputDir;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
 
        bool abort;
 };