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[mothur.git] / parsimony.h

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+#ifndef PARSIMONY_H
+#define PARSIMONY_H
+
+
+/*
+ *  parsimony.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 1/26/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "treecalculator.h"
+#include "treemap.h"
+
+/***********************************************************************/
+
+class Parsimony : public TreeCalculator  {
+       
+       public:
+               Parsimony() {};
+               ~Parsimony() {};
+               EstOutput getValues(Tree*, int, string);
+               
+       private:
+               struct linePair {
+                       int start;
+                       int num;
+                       linePair(int i, int j) : start(i), num(j) {}
+               };
+               vector<linePair> lines;
+       
+               EstOutput data;
+               int processors;
+               string outputDir;
+       
+               EstOutput driver(Tree*, vector< vector<string> >, int, int, TreeMap*); 
+               EstOutput createProcesses(Tree*, vector< vector<string> >, TreeMap*);
+};
+
+/***********************************************************************/
+
+#endif