added root parameter to the unifrac commands so you can choose to include the entire...

[mothur.git] / weighted.h

diff --git a/weighted.h b/weighted.h
index 3fa5123a59363ce4697fbead42522e35b78667b9..d78edf4d49ffd17e24f8eb559747a43952ad522a 100644 (file)
--- a/weighted.h
+++ b/weighted.h
@@ -19,14 +19,12 @@
 class Weighted : public TreeCalculator  {
        
        public:
-               Weighted(TreeMap* t) : tmap(t) {};
+               Weighted(TreeMap* t, bool r) : tmap(t), includeRoot(r) {};
                ~Weighted() {};
                
-               EstOutput getValues(Tree*, string, string, vector<double>&);
+               EstOutput getValues(Tree*, string, string);
                EstOutput getValues(Tree*, int, string);
                
-               vector<double> getBranchLengthSums(Tree*);
-               
        private:
                struct linePair {
                        int start;
@@ -42,9 +40,12 @@ class Weighted : public TreeCalculator  {
                map<string, double> WScore; //a score for each group combination i.e. AB, AC, BC.
                int processors;
                string outputDir;
+               map< vector<string>, set<int> > rootForGrouping;  //maps a grouping combo to the root for that combo
+               bool includeRoot;
                
-               EstOutput driver(Tree*, vector< vector<string> >, int, int, vector<double>&); 
-               EstOutput createProcesses(Tree*, vector< vector<string> >, vector<double>&);
+               EstOutput driver(Tree*, vector< vector<string> >, int, int); 
+               EstOutput createProcesses(Tree*, vector< vector<string> >);
+               double getLengthToRoot(Tree*, int, string, string);
 };
 
 /***********************************************************************/