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

[mothur.git] / getrabundcommand.h

diff --git a/getrabundcommand.h b/getrabundcommand.h
index ed51be12ca9e9c0a41b9c03a5089cd9fce7b3893..e853ac5f913a1d758e7a633510478ad30449feec 100644 (file)
--- a/getrabundcommand.h
+++ b/getrabundcommand.h
@@ -21,7 +21,12 @@ class GlobalData;
 class GetRAbundCommand : public Command {
 public:
        GetRAbundCommand(string);
+       GetRAbundCommand();
        ~GetRAbundCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -33,6 +38,8 @@ private:
        InputData* input;
        ListVector* list;
        RAbundVector* rabund;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
 
        bool abort, allLines, sorted;
        set<string> labels; //holds labels to be used