X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimony.h;h=b116aa2d1a55e0ba84571f1f4c9500c6be5d8fcc;hb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;hp=74ebefdc2d185eaa325a8ec4beff12fc04733cff;hpb=f099fdc1e3a0d7b75d780a164e5bdb93496a7a1d;p=mothur.git

diff --git a/parsimony.h b/parsimony.h
index 74ebefd..b116aa2 100644
--- a/parsimony.h
+++ b/parsimony.h
@@ -13,7 +13,6 @@
 
 #include "treecalculator.h"
 #include "treemap.h"
-#include "globaldata.hpp"
 
 /***********************************************************************/
 
@@ -22,15 +21,24 @@ 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;
-		Tree* copyTree;
+		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> >);
 };
 
 /***********************************************************************/