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

[mothur.git] / chimeraccodecommand.h

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
index d980288ac3585916321edec15114d0c47303e120..a9ed223b112cdb50876024c893257549e159481f 100644 (file)
--- a/chimeraccodecommand.h
+++ b/chimeraccodecommand.h
@@ -20,7 +20,12 @@
 class ChimeraCcodeCommand : public Command {
 public:
        ChimeraCcodeCommand(string);
+       ChimeraCcodeCommand();
        ~ChimeraCcodeCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -47,6 +52,7 @@ private:
        Chimera* chimera;
        vector<string> fastaFileNames;
        vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        
 };