consensuscommand.h

   1 #ifndef CONCENSUSCOMMAND_H
   2 #define CONCENSUSCOMMAND_H
   3 /*
   4  *  consensuscommand.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(string);
  23         ~ConcensusCommand();
  24         int execute();
  25         void help();
  26
  27 private:
  28         GlobalData* globaldata;
  29         SharedUtil* util;
  30         vector<Tree*> t;
  31         Tree* consensusTree;
  32         bool abort;
  33         vector<string> treeSet;         //set containing all members of the tree to start recursion.  filled in getSets().
  34         map< vector<string>, int > nodePairs;  //<map of possible combinations these combos are the pcounts or descendants info, to how many times they occured
  35                                                                                 // ie. combos FI and EGK would create nodePairs[vector containing F and I] = 1; nodePairs[vector containing E, G and K] = 1
  36                                                                                 // if you saw the combo FI again in another tree you would then update nodePairs[vector containing F and I] = 2;
  37                                                                                 // requires vectors to be sorted to find key.
  38         map< vector<string>, vector< vector<string> > > bestSplit;  //maps a group to its best split
  39         map< vector<string>, int > nodePairsInitialRate;
  40         map< vector<string>, int > nodePairsInTree;
  41         map<string, int>::iterator it;
  42         map< vector<string>, int>::iterator it2;
  43         string outputFile, notIncluded, filename;
  44         ofstream out, out2;
  45         int numNodes, numLeaves, count;  //count is the next available spot in the tree vector
  46
  47         int getSets();
  48         int getSubgroupRating(vector<string>);
  49         vector<string> getSmallest(map< vector<string>, int>);
  50         vector<string> getNextAvailableSet(vector<string>, vector<string>&);
  51         vector<string> getRestSet(vector<string>, vector<string>);
  52         bool isSubset(vector<string>, vector<string>);
  53         int findSpot(string);
  54         int buildConcensusTree(vector<string>);
  55
  56 };
  57
  58 #endif
  59