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 ConcensusCommand : public Command {
  18
  19 public:
  20         ConcensusCommand(string);
  21         ConcensusCommand();
  22         ~ConcensusCommand() {}
  23
  24         vector<string> setParameters();
  25         string getCommandName()                 { return "concensus";   }
  26         string getCommandCategory()             { return "Hidden";              }
  27         string getHelpString();
  28         string getCitation() { return "no citation"; }
  29
  30         int execute();
  31         void help() { m->mothurOut(getHelpString()); }
  32
  33
  34 private:
  35         SharedUtil* util;
  36         vector<Tree*> t;
  37         Tree* consensusTree;
  38         bool abort;
  39         vector<string> treeSet;         //set containing all members of the tree to start recursion.  filled in getSets().
  40         map< vector<string>, int > nodePairs;  //<map of possible combinations these combos are the pcounts or descendants info, to how many times they occured
  41                                                                                 // ie. combos FI and EGK would create nodePairs[vector containing F and I] = 1; nodePairs[vector containing E, G and K] = 1
  42                                                                                 // if you saw the combo FI again in another tree you would then update nodePairs[vector containing F and I] = 2;
  43                                                                                 // requires vectors to be sorted to find key.
  44         map< vector<string>, vector< vector<string> > > bestSplit;  //maps a group to its best split
  45         map< vector<string>, int > nodePairsInitialRate;
  46         map< vector<string>, int > nodePairsInTree;
  47         map<string, int>::iterator it;
  48         map< vector<string>, int>::iterator it2;
  49         string outputFile, notIncluded, filename;
  50         ofstream out, out2;
  51         int numNodes, numLeaves, count;  //count is the next available spot in the tree vector
  52         vector<string> outputNames;
  53
  54         int getSets();
  55         int getSubgroupRating(vector<string>);
  56         vector<string> getSmallest(map< vector<string>, int>);
  57         vector<string> getNextAvailableSet(vector<string>, vector<string>&);
  58         vector<string> getRestSet(vector<string>, vector<string>);
  59         bool isSubset(vector<string>, vector<string>);
  60         int findSpot(string);
  61         int buildConcensusTree(vector<string>);
  62
  63 };
  64
  65 #endif
  66