fixed craig nelsons weighted bug and paralellized parsimony

[mothur.git] / parsimony.h

diff --git a/parsimony.h b/parsimony.h
index 74ebefdc2d185eaa325a8ec4beff12fc04733cff..fc905f2d3c432ab1ce4a05007e13ca0f14264fd0 100644 (file)
--- 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> >);
 };
 
 /***********************************************************************/