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

[mothur.git] / preclustercommand.h

diff --git a/preclustercommand.h b/preclustercommand.h
index de6a5727575a7f35d2605239968a37435faa388f..7bbb5a7f448351d1bf72616e3c40f7f10b41eda4 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -31,7 +31,12 @@ class PreClusterCommand : public Command {
        
 public:
        PreClusterCommand(string);
+       PreClusterCommand();
        ~PreClusterCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
@@ -44,6 +49,8 @@ private:
        map<string, int> sizes;  //this map a seq name to the number of identical seqs in the names file
        map<string, int>::iterator itSize; 
 //     map<string, bool> active; //maps sequence name to whether it has already been merged or not.
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        int readFASTA();
        void readNameFile();