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

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index bf463a00d238cd6da3b21213f0d393ee6ff895c9..3b2d345d73fc46244446cd136366869f92a6e6d6 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -21,7 +21,12 @@ class DistanceCommand : public Command {
 
 public:
        DistanceCommand(string);
+       DistanceCommand();
        ~DistanceCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
@@ -42,7 +47,8 @@ private:
        vector<linePair*> lines;
        
        bool abort;
-       vector<string>  Estimators; //holds estimators to be used
+       vector<string>  Estimators, outputNames; //holds estimators to be used
+       map<string, vector<string> > outputTypes;
        
        //void m->appendFiles(string, string);
        void createProcesses(string);