X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimony.h;h=fc905f2d3c432ab1ce4a05007e13ca0f14264fd0;hb=c53ef46b40b97c00e32bfd8c3924ce8c51b5cd7b;hp=74ebefdc2d185eaa325a8ec4beff12fc04733cff;hpb=3fd6dd6e4f19a458ac2966ee5458787e998a1bde;p=mothur.git

diff --git a/parsimony.h b/parsimony.h
index 74ebefd..fc905f2 100644
--- a/parsimony.h
+++ b/parsimony.h
@@ -22,15 +22,25 @@ 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:
+		struct linePair {
+			int start;
+			int num;
+			linePair(int i, int j) : start(i), num(j) {}
+		};
+		vector<linePair> lines;
+	
 		GlobalData* globaldata;
-		Tree* copyTree;
 		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> >);
 };
 
 /***********************************************************************/