sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / parsimony.h

diff --git a/parsimony.h b/parsimony.h
index fc905f2d3c432ab1ce4a05007e13ca0f14264fd0..bf0e0d4f90198ef353c2c1899414f699454c8a7e 100644 (file)
--- a/parsimony.h
+++ b/parsimony.h
@@ -12,18 +12,16 @@
  */
 
 #include "treecalculator.h"
-#include "treemap.h"
-#include "globaldata.hpp"
+#include "counttable.h"
 
 /***********************************************************************/
 
 class Parsimony : public TreeCalculator  {
        
        public:
-               Parsimony(TreeMap* t) : tmap(t) {};
+               Parsimony() {};
                ~Parsimony() {};
                EstOutput getValues(Tree*, int, string);
-               //EstOutput getValues(Tree*, string, string) { return data; }
                
        private:
                struct linePair {
@@ -33,14 +31,12 @@ class Parsimony : public TreeCalculator  {
                };
                vector<linePair> lines;
        
-               GlobalData* globaldata;
                EstOutput data;
-               TreeMap* tmap;
                int processors;
                string outputDir;
        
-               EstOutput driver(Tree*, vector< vector<string> >, int, int); 
-               EstOutput createProcesses(Tree*, vector< vector<string> >);
+               EstOutput driver(Tree*, vector< vector<string> >, int, int, CountTable*); 
+               EstOutput createProcesses(Tree*, vector< vector<string> >, CountTable*);
 };
 
 /***********************************************************************/