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

[mothur.git] / sensspeccommand.h

diff --git a/sensspeccommand.h b/sensspeccommand.h
index 818667a1c52729a2610564334d13225472eaac39..687834c5b1b9098830747b79dd0e9e6135e6951b 100644 (file)
--- a/sensspeccommand.h
+++ b/sensspeccommand.h
@@ -18,7 +18,12 @@ class SensSpecCommand : public Command {
        
 public:
        SensSpecCommand(string);
+       SensSpecCommand();
        ~SensSpecCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -31,6 +36,8 @@ private:
        string listFile, distFile, nameFile, sensSpecFileName;
        string outputDir;
        string format;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
 
        long int truePositives, falsePositives, trueNegatives, falseNegatives;
        bool abort;