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

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index c5ef88885d9b4c1e7275c998e8a2b35bbbbba99b..aa9b5e7102a324bce97095c2fce7d78f470ab3fc 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -20,7 +20,12 @@
 class ChimeraSlayerCommand : public Command {
 public:
        ChimeraSlayerCommand(string);
+       ChimeraSlayerCommand();
        ~ChimeraSlayerCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -50,6 +55,7 @@ private:
        Chimera* chimera;
        
        vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        vector<string> fastaFileNames;
        
 };