working on nmds command

[mothur.git] / consensuscommand.h

diff --git a/consensuscommand.h b/consensuscommand.h
index 145bea5bdaf24410229cb42e889e7f02cacdd9c8..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();    
        
@@ -43,8 +48,10 @@ 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;
                                                                                
-       void getSets();
+       int getSets();
        int getSubgroupRating(vector<string>);
        vector<string> getSmallest(map< vector<string>, int>);
        vector<string> getNextAvailableSet(vector<string>, vector<string>&);