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

[mothur.git] / unweighted.h

diff --git a/unweighted.h b/unweighted.h
index e3bf3a8fc240648e4a38f48ced539845d3648706..0ccfab55ad9500f46f33d74e1c1c19f95ec525ba 100644 (file)
--- a/unweighted.h
+++ b/unweighted.h
@@ -19,21 +19,34 @@
 class Unweighted : public TreeCalculator  {
        
        public:
-               Unweighted(TreeMap* t) : tmap(t) {};
+               Unweighted(TreeMap* t, bool r) : tmap(t), includeRoot(r) {};
                ~Unweighted() {};
-               EstOutput getValues(Tree*);
+               EstOutput getValues(Tree*, int, string);
+               EstOutput getValues(Tree*, string, string, int, string);
                
        private:
+               struct linePair {
+                       int start;
+                       int num;
+                       linePair(int i, int j) : start(i), num(j) {}
+               };
+               vector<linePair> lines;
+               
                GlobalData* globaldata;
                EstOutput data;
-               vector<int> penalty;
                TreeMap* tmap;
-               bool inUsersGroups(string);
-
+               int processors;
+               string outputDir;
+               map< vector<string>, set<int> > rootForGrouping;  //maps a grouping combo to the roots for that combo
+               bool includeRoot;
+               
+               EstOutput driver(Tree*, vector< vector<string> >, int, int); 
+               EstOutput createProcesses(Tree*, vector< vector<string> >);
+               EstOutput driver(Tree*, vector< vector<string> >, int, int, bool); 
+               EstOutput createProcesses(Tree*, vector< vector<string> >, bool);
+               int getRoot(Tree*, int, vector<string>);
 };
 
 /***********************************************************************/
 
-
-
-#endif
\ No newline at end of file
+#endif