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

[mothur.git] / parsesffcommand.h

diff --git a/parsesffcommand.h b/parsesffcommand.h
index 5714e0df851abd68cd52cbd195e0f10fc61a69fa..9dfa083369d2241b428709119e2c2508bd667867 100644 (file)
--- a/parsesffcommand.h
+++ b/parsesffcommand.h
@@ -16,7 +16,12 @@
 class ParseSFFCommand : public Command {
 public:
        ParseSFFCommand(string);
+       ParseSFFCommand();
        ~ParseSFFCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();    
        
@@ -42,6 +47,7 @@ private:
        map<string, int> barcodes;
        vector<string> groupVector;
        vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
 
 //     string stripSeqQual(string, int, int);
 //     string stripQualQual(string, int, int);