fix trim.seqs / qualscores bug

[mothur.git] / unweighted.h

diff --git a/unweighted.h b/unweighted.h
index f41326115020013fb2e59df755bff1e961001c8d..0ccfab55ad9500f46f33d74e1c1c19f95ec525ba 100644 (file)
--- a/unweighted.h
+++ b/unweighted.h
@@ -19,7 +19,7 @@
 class Unweighted : public TreeCalculator  {
        
        public:
-               Unweighted(TreeMap* t) : tmap(t) {};
+               Unweighted(TreeMap* t, bool r) : tmap(t), includeRoot(r) {};
                ~Unweighted() {};
                EstOutput getValues(Tree*, int, string);
                EstOutput getValues(Tree*, string, string, int, string);
@@ -37,12 +37,14 @@ class Unweighted : public TreeCalculator  {
                TreeMap* tmap;
                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>);
 };
 
 /***********************************************************************/