added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / parsimony.h

diff --git a/parsimony.h b/parsimony.h
index ebe3d8d89d4ecf2174dc84f8796245a07f4384c9..b116aa2d1a55e0ba84571f1f4c9500c6be5d8fcc 100644 (file)
--- a/parsimony.h
+++ b/parsimony.h
@@ -13,7 +13,6 @@
 
 #include "treecalculator.h"
 #include "treemap.h"
-#include "globaldata.hpp"
 
 /***********************************************************************/
 
@@ -22,14 +21,26 @@ class Parsimony : public TreeCalculator  {
        public:
                Parsimony(TreeMap* t) : tmap(t) {};
                ~Parsimony() {};
-               EstOutput getValues(Tree*);
+               EstOutput getValues(Tree*, int, string);
+               //EstOutput getValues(Tree*, string, string) { return data; }
                
        private:
-               GlobalData* globaldata;
+               struct linePair {
+                       int start;
+                       int num;
+                       linePair(int i, int j) : start(i), num(j) {}
+               };
+               vector<linePair> lines;
+       
                EstOutput data;
                TreeMap* tmap;
-               map<string, int>::iterator it;
+               int processors;
+               string outputDir;
+       
+               EstOutput driver(Tree*, vector< vector<string> >, int, int); 
+               EstOutput createProcesses(Tree*, vector< vector<string> >);
 };
 
 /***********************************************************************/
-#endif
\ No newline at end of file
+
+#endif