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

[mothur.git] / parsefastaqcommand.h

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index 071077577f1bec0fb39b05a6d18b01917e7a839e..c45405f42455de7bbdf93d7f2c391756d0700a05 100644 (file)
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -17,13 +17,19 @@ class ParseFastaQCommand : public Command {
 
 public:
        ParseFastaQCommand(string);
+       ParseFastaQCommand();
        ~ParseFastaQCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();    
        
 private:
 
        vector<string> outputNames;     
+       map<string, vector<string> > outputTypes;
        string outputDir, fastaQFile;
        bool abort;