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

[mothur.git] / treegroupscommand.h

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 3e8fbb01c4df3c34540a11342a5a960a03788145..c61c9fbfa63bf84a2482955ca20aa914f89b9400 100644 (file)
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -35,7 +35,12 @@ class TreeGroupCommand : public Command {
        
 public:
        TreeGroupCommand(string);       
+       TreeGroupCommand();
        ~TreeGroupCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
@@ -64,6 +69,7 @@ private:
        int numGroups;
        ofstream out;
        float precision, cutoff;
+       map<string, vector<string> > outputTypes;
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used