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

[mothur.git] / normalizesharedcommand.h

diff --git a/normalizesharedcommand.h b/normalizesharedcommand.h
index fcfc727b23ba0e4aae0fc1d1406c6799fde81689..22158bd6d5ff136d0df81d0304b476ec580b8b7a 100644 (file)
--- a/normalizesharedcommand.h
+++ b/normalizesharedcommand.h
@@ -21,7 +21,12 @@ class NormalizeSharedCommand : public Command {
 
 public:
        NormalizeSharedCommand(string);
+       NormalizeSharedCommand();
        ~NormalizeSharedCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -35,7 +40,8 @@ private:
        set<string> labels; //holds labels to be used
        string groups, label, outputDir, method;
        int norm;
-       vector<string> Groups;
+       vector<string> Groups, outputNames;
+       map<string, vector<string> > outputTypes;
        
        int normalize(vector<SharedRAbundVector*>&, ofstream&);
        int eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup);