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

[mothur.git] / parselistscommand.h

diff --git a/parselistscommand.h b/parselistscommand.h
index c765bcdd86c34c89b688685969e89d55928809f6..5ecc7ab13205d4f34d7c496a6b2cc3221615eafe 100644 (file)
--- a/parselistscommand.h
+++ b/parselistscommand.h
@@ -19,8 +19,13 @@
 class ParseListCommand : public Command {
        
 public:
-       ParseListCommand(string);       
+       ParseListCommand(string);
+       ParseListCommand();     
        ~ParseListCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
@@ -35,6 +40,8 @@ private:
        string outputDir, listfile, groupfile, label;
        set<string> labels;
        bool abort, allLines;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        map<string, ofstream*> filehandles;
        map<string, ofstream*>::iterator it3;