removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / weighted.h

diff --git a/weighted.h b/weighted.h
index 41b738b00be222d8f7075af9a0621733c6bcf2fc..c23a11599b4b8d74fdfacd05a5a02ae727834455 100644 (file)
--- a/weighted.h
+++ b/weighted.h
@@ -19,20 +19,35 @@
 class Weighted : public TreeCalculator  {
        
        public:
-               Weighted(TreeMap* t) : tmap(t) {};
+               Weighted(TreeMap* t, bool r) : tmap(t), includeRoot(r) {};
                ~Weighted() {};
-               EstOutput getValues(Tree*);
+               
                EstOutput getValues(Tree*, string, string);
+               EstOutput getValues(Tree*, int, string);
                
        private:
-               GlobalData* globaldata;
+               struct linePair {
+                       int start;
+                       int num;
+                       linePair(int i, int j) : start(i), num(j) {}
+               };
+               vector<linePair> lines;
+
                EstOutput data;
                TreeMap* tmap;
                map<string, int>::iterator it;
-               map<string, float> WScore; //a score for each group combination i.e. AB, AC, BC.
+               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); 
+               EstOutput createProcesses(Tree*, vector< vector<string> >);
+               double getLengthToRoot(Tree*, int, string, string);
 };
 
 /***********************************************************************/
 
 
-#endif
\ No newline at end of file
+#endif