concensuscommand.h

   1 #ifndef CONCENSUSCOMMAND_H
   2 #define CONCENSUSCOMMAND_H
   3 /*
   4  *  concensuscommand.h
   5  *  Mothur
   6  *
   7  *  Created by Sarah Westcott on 4/29/09.
   8  *  Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
   9  *
  10  */
  11
  12 #include "command.hpp"
  13 #include "tree.h"
  14 #include "treemap.h"
  15 #include "sharedutilities.h"
  16
  17 class GlobalData;
  18
  19 class ConcensusCommand : public Command {
  20
  21 public:
  22         ConcensusCommand();
  23         ~ConcensusCommand();
  24         int execute();
  25
  26 private:
  27         GlobalData* globaldata;
  28         SharedUtil* util;
  29         vector<Tree*> t;
  30         Tree* concensusTree;
  31         vector< map<string, int> > nodePairs;  //<maps a pair of nodes joined, number of times that pair occurred>      -one entry in vector for each internal node.
  32                                                                                 // i.e. if node 7's child pairs are 1,2 ten times and 1,3 20 times then the map would be [12, 10] and [13, 20];
  33         map<string, int>::iterator it;
  34         map<string, int>::iterator it2;
  35         string outputFile, notIncluded;
  36         ofstream out, out2;
  37         int numNodes, numLeaves;
  38
  39         void getNames(string, string&, string&);
  40 };
  41
  42 #endif
  43