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

[mothur.git] / rarefactcommand.h

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 3cf0ef7f4cf68a5976d67dfe9cc4c9a9f0c7d57c..7da0b2f9f5301d80302d97f7da23d1cd8fee12c1 100644 (file)
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -23,8 +23,13 @@ class GlobalData;
 class RareFactCommand : public Command {
        
 public:
-       RareFactCommand(string);        
+       RareFactCommand(string);
+       RareFactCommand();      
        ~RareFactCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();    
        
@@ -43,8 +48,9 @@ private:
        set<string> labels; //holds labels to be used
        string label, calc;
        vector<string>  Estimators;
-       vector<string> inputFileNames;
+       vector<string> inputFileNames, outputNames;
        vector<string> groups;
+       map<string, vector<string> > outputTypes;
        string outputDir;
        
        vector<string> parseSharedFile(string);