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

[mothur.git] / readtreecommand.h

diff --git a/readtreecommand.h b/readtreecommand.h
index 5d5b9b5eb74f17983d58fd55610218d2c23a8866..97391d0982bbadb437ebe13318c47babeca4a981 100644 (file)
--- a/readtreecommand.h
+++ b/readtreecommand.h
@@ -19,7 +19,12 @@ class GlobalData;
 class ReadTreeCommand : public Command {
 public:
        ReadTreeCommand(string);
+       ReadTreeCommand() {}
        ~ReadTreeCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -30,6 +35,8 @@ private:
        string filename, treefile, groupfile, namefile;
        bool abort;
        map<string, string> nameMap;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        int readNamesFile();
        int numUniquesInName;