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

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 8099a3998c1a63de92d9c72b2c5419c08e2f96ff..874e43ce5a8f45178a073b9d8e8e00fa8852deb0 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -39,7 +39,12 @@ class GetOTURepCommand : public Command {
 
 public:
        GetOTURepCommand(string);
+       GetOTURepCommand();
        ~GetOTURepCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
 
@@ -66,6 +71,7 @@ private:
        vector<SeqMap> seqVec;                  // contains maps with sequence index and distance
                                                                        // for all distances related to a certain sequence
        vector<int> rowPositions;
+       map<string, vector<string> > outputTypes;
 
        void readNamesFile();
        int process(ListVector*);