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

[mothur.git] / collectcommand.h

diff --git a/collectcommand.h b/collectcommand.h
index 773bdae5c1d0b71bdad01e4403d3af3702274e70..20c863b81dfd79fad597cd6e1e83571256873969 100644 (file)
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -38,7 +38,12 @@ class CollectCommand : public Command {
        
 public:
        CollectCommand(string); 
+       CollectCommand();
        ~CollectCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
@@ -52,6 +57,8 @@ private:
        vector<Display*> cDisplays;
        int abund, size;
        float freq;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used