sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / unweighted.h

diff --git a/unweighted.h b/unweighted.h
index f41326115020013fb2e59df755bff1e961001c8d..b136b007b517e56645be544ee6556f83a45de649 100644 (file)
--- a/unweighted.h
+++ b/unweighted.h
@@ -12,14 +12,14 @@
  */
 
 #include "treecalculator.h"
-#include "treemap.h"
+#include "counttable.h"
 
 /***********************************************************************/
 
 class Unweighted : public TreeCalculator  {
        
        public:
-               Unweighted(TreeMap* t) : tmap(t) {};
+        Unweighted(bool r) : includeRoot(r) {};
                ~Unweighted() {};
                EstOutput getValues(Tree*, int, string);
                EstOutput getValues(Tree*, string, string, int, string);
@@ -32,17 +32,17 @@ class Unweighted : public TreeCalculator  {
                };
                vector<linePair> lines;
                
-               GlobalData* globaldata;
                EstOutput data;
-               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);
-
+               EstOutput driver(Tree*, vector< vector<string> >, int, int, CountTable*); 
+               EstOutput createProcesses(Tree*, vector< vector<string> >, CountTable*);
+               EstOutput driver(Tree*, vector< vector<string> >, int, int, bool, CountTable*); 
+               EstOutput createProcesses(Tree*, vector< vector<string> >, bool, CountTable*);
+               int getRoot(Tree*, int, vector<string>);
 };
 
 /***********************************************************************/