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

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 6fa1914f31e320517ff89389a34fc3e5a1cd6dc6..04acd302891f36df23399ac9d9b1694535c7005e 100644 (file)
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -23,7 +23,12 @@ class ParsimonyCommand : public Command {
 
 public:
        ParsimonyCommand(string);       
+       ParsimonyCommand();
        ~ParsimonyCommand() { if (abort == false) { delete pars; delete util; delete output; }  }
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
 
@@ -57,6 +62,7 @@ private:
        bool abort;
        string groups, itersString;
        vector<string> Groups, outputNames; //holds groups to be used
+       map<string, vector<string> > outputTypes;
 
        void printParsimonyFile();  
        int printUSummaryFile();