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

[mothur.git] / sharedcommand.h

diff --git a/sharedcommand.h b/sharedcommand.h
index 0f3e7ef2289b39f9ab4807ccda5cbe179ff51d04..2c5ab237a2d39b006dee4eca4e9b9b2c65a57ebe 100644 (file)
--- a/sharedcommand.h
+++ b/sharedcommand.h
@@ -27,7 +27,12 @@ class SharedCommand : public Command {
        
 public:
        SharedCommand(string);  
+       SharedCommand();
        ~SharedCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help() {}
        
@@ -37,6 +42,7 @@ private:
        int readOrderFile();
        bool isValidGroup(string, vector<string>);
        int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
+       map<string, vector<string> > outputTypes;
        
        GlobalData* globaldata;
        ReadOTUFile* read;