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

[mothur.git] / chimeracheckcommand.h

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index 71e1f0cdad86dc4610a65711c57c355eb9ee2aaf..6e81812e469772b18a737930354f1bdf943a9ef9 100644 (file)
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -21,7 +21,12 @@
 class ChimeraCheckCommand : public Command {
 public:
        ChimeraCheckCommand(string);
+       ChimeraCheckCommand();
        ~ChimeraCheckCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -51,6 +56,7 @@ private:
        vector<string> fastaFileNames;
        vector<string> nameFileNames;
        vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
                
 };