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

[mothur.git] / consensuscommand.h

diff --git a/consensuscommand.h b/consensuscommand.h
index 7a7960708c9b5d17d69355caaf8cfd8be089e76d..d5072da082cd020d1836e39c06228fa4689eafbe 100644 (file)
--- a/consensuscommand.h
+++ b/consensuscommand.h
@@ -20,7 +20,12 @@ class ConcensusCommand : public Command {
        
 public:
        ConcensusCommand(string);       
+       ConcensusCommand();
        ~ConcensusCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();    
        
@@ -43,6 +48,8 @@ private:
        string outputFile, notIncluded, filename;
        ofstream out, out2;
        int numNodes, numLeaves, count;  //count is the next available spot in the tree vector
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
                                                                                
        int getSets();
        int getSubgroupRating(vector<string>);