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

[mothur.git] / clusterfragmentscommand.h

diff --git a/clusterfragmentscommand.h b/clusterfragmentscommand.h
index 9bdbc4479f19bd7e1aa8297ed4e1f278e0de912f..842485e15c1c9679cf6cd8b1cb16f987454a27c5 100644 (file)
--- a/clusterfragmentscommand.h
+++ b/clusterfragmentscommand.h
@@ -31,7 +31,12 @@ class ClusterFragmentsCommand : public Command {
        
 public:
        ClusterFragmentsCommand(string);
+       ClusterFragmentsCommand();
        ~ClusterFragmentsCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
@@ -42,6 +47,8 @@ private:
        map<string, string> names; //represents the names file first column maps to second column
        map<string, int> sizes;  //this map a seq name to the number of identical seqs in the names file
        map<string, int>::iterator itSize; 
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        int readFASTA();
        void readNameFile();