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

[mothur.git] / readotucommand.h

diff --git a/readotucommand.h b/readotucommand.h
index bf9ccc00d0e7151ea4dce787b42265f092416bbd..eb0ca8f7832e5f1877a172fa0449a3ae29e5416f 100644 (file)
--- a/readotucommand.h
+++ b/readotucommand.h
@@ -20,7 +20,12 @@ class GlobalData;
 class ReadOtuCommand : public Command {
 public:
        ReadOtuCommand(string);
+       ReadOtuCommand();
        ~ReadOtuCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -30,7 +35,8 @@ private:
        Command* shared;
        GroupMap* groupMap;
        string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups, outputDir, ordergroupfile, relAbundfile;
-       vector<string> Groups;
+       vector<string> Groups, outputNames;
+       map<string, vector<string> > outputTypes;
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used