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

[mothur.git] / otuhierarchycommand.h

diff --git a/otuhierarchycommand.h b/otuhierarchycommand.h
index 1cd427f1a7af8442d4747e65662bbf431ccdcbbd..dd5f3a7adc759733bf3972392485c79b94669977 100644 (file)
--- a/otuhierarchycommand.h
+++ b/otuhierarchycommand.h
@@ -18,7 +18,12 @@ class OtuHierarchyCommand : public Command {
 
 public:
        OtuHierarchyCommand(string);
+       OtuHierarchyCommand();
        ~OtuHierarchyCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -26,6 +31,8 @@ private:
        bool abort;
        set<string> labels; //holds labels to be used
        string label, listFile, outputDir, output;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        vector<ListVector> getListVectors();