parsimony.h

   1 #ifndef PARSIMONY_H
   2 #define PARSIMONY_H
   3
   4
   5 /*
   6  *  parsimony.h
   7  *  Mothur
   8  *
   9  *  Created by Sarah Westcott on 1/26/09.
  10  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  11  *
  12  */
  13
  14 #include "treecalculator.h"
  15 #include "treemap.h"
  16 #include "globaldata.hpp"
  17
  18 /***********************************************************************/
  19
  20 class Parsimony : public TreeCalculator  {
  21
  22         public:
  23                 Parsimony(TreeMap* t) : tmap(t) {};
  24                 ~Parsimony() {};
  25                 EstOutput getValues(Tree*, int, string);
  26                 //EstOutput getValues(Tree*, string, string) { return data; }
  27
  28         private:
  29                 struct linePair {
  30                         int start;
  31                         int num;
  32                         linePair(int i, int j) : start(i), num(j) {}
  33                 };
  34                 vector<linePair> lines;
  35
  36                 GlobalData* globaldata;
  37                 EstOutput data;
  38                 TreeMap* tmap;
  39                 int processors;
  40                 string outputDir;
  41
  42                 EstOutput driver(Tree*, vector< vector<string> >, int, int);
  43                 EstOutput createProcesses(Tree*, vector< vector<string> >);
  44 };
  45
  46 /***********************************************************************/
  47
  48 #endif