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

[mothur.git] / chimerabellerophoncommand.h

diff --git a/chimerabellerophoncommand.h b/chimerabellerophoncommand.h
index 4ff7f799202f9403b8793a625ee0a551354a69a2..6e1ae50794f23d92c75d0224011251e385ae8f43 100644 (file)
--- a/chimerabellerophoncommand.h
+++ b/chimerabellerophoncommand.h
@@ -20,7 +20,12 @@
 class ChimeraBellerophonCommand : public Command {
 public:
        ChimeraBellerophonCommand(string);
+       ChimeraBellerophonCommand();
        ~ChimeraBellerophonCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map< string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
                
@@ -31,6 +36,7 @@ private:
        int processors, window, increment, numSeqs;
        Chimera* chimera;
        vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        vector<string> fastaFileNames;
 };