sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / unweighted.h

diff --git a/unweighted.h b/unweighted.h
index 007fef7911918ba7c6505f8fc1213cdd8e9be43a..b136b007b517e56645be544ee6556f83a45de649 100644 (file)
--- a/unweighted.h
+++ b/unweighted.h
@@ -12,24 +12,37 @@
  */
 
 #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*);
-               EstOutput getValues(Tree*, string, string);
+               EstOutput getValues(Tree*, int, string);
+               EstOutput getValues(Tree*, string, string, int, string);
                
        private:
-               GlobalData* globaldata;
-               Tree* copyTree;
+               struct linePair {
+                       int start;
+                       int num;
+                       linePair(int i, int j) : start(i), num(j) {}
+               };
+               vector<linePair> lines;
+               
                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, 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>);
 };
 
 /***********************************************************************/