mods in testing 1.16.0

[mothur.git] / readotucommand.h

diff --git a/readotucommand.h b/readotucommand.h
index 543642b66b4bd4b889fd54c8d19776fc71b17b8d..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();
        
@@ -29,8 +34,9 @@ private:
        InputData* input;
        Command* shared;
        GroupMap* groupMap;
-       string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups;
-       vector<string> Groups;
+       string filename, listfile, orderfile, sharedfile, label, groupfile, sabundfile, rabundfile, format, groups, outputDir, ordergroupfile, relAbundfile;
+       vector<string> Groups, outputNames;
+       map<string, vector<string> > outputTypes;
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used