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

[mothur.git] / getrelabundcommand.h

diff --git a/getrelabundcommand.h b/getrelabundcommand.h
index 9725a31ab546f0829ec4ca0bf370e6792fdfeadf..3a5f6ad094a16bf2e43c4521c2f1d35436352e60 100644 (file)
--- a/getrelabundcommand.h
+++ b/getrelabundcommand.h
@@ -21,7 +21,12 @@ class GetRelAbundCommand : public Command {
 
 public:
        GetRelAbundCommand(string);
+       GetRelAbundCommand();
        ~GetRelAbundCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -34,7 +39,8 @@ private:
        bool abort, allLines, pickedGroups;
        set<string> labels; //holds labels to be used
        string groups, label, outputDir, scale;
-       vector<string> Groups;
+       vector<string> Groups, outputNames;
+       map<string, vector<string> > outputTypes;
        
        int getRelAbundance(vector<SharedRAbundVector*>&, ofstream&);
        int eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup);