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 "consensus";   }
  26         string getCommandCategory()             { return "Hidden";              }
  27         string getHelpString();
  28         string getCitation() { return "no citation"; }
  29         string getDescription()         { return "consensus"; }
  30
  31         int execute();
  32         void help() { m->mothurOut(getHelpString()); }
  33
  34
  35 private:
  36         SharedUtil* util;
  37         vector<Tree*> t;
  38         Tree* consensusTree;
  39         bool abort;
  40         vector<string> treeSet;         //set containing all members of the tree to start recursion.  filled in getSets().
  41         map< vector<string>, int > nodePairs;  //<map of possible combinations these combos are the pcounts or descendants info, to how many times they occured
  42                                                                                 // ie. combos FI and EGK would create nodePairs[vector containing F and I] = 1; nodePairs[vector containing E, G and K] = 1
  43                                                                                 // if you saw the combo FI again in another tree you would then update nodePairs[vector containing F and I] = 2;
  44                                                                                 // requires vectors to be sorted to find key.
  45         map< vector<string>, vector< vector<string> > > bestSplit;  //maps a group to its best split
  46         map< vector<string>, int > nodePairsInitialRate;
  47         map< vector<string>, int > nodePairsInTree;
  48         map<string, int>::iterator it;
  49         map< vector<string>, int>::iterator it2;
  50         string outputFile, notIncluded, filename;
  51         ofstream out, out2;
  52         int numNodes, numLeaves, count;  //count is the next available spot in the tree vector
  53         vector<string> outputNames;
  54
  55         int getSets();
  56         int getSubgroupRating(vector<string>);
  57         vector<string> getSmallest(map< vector<string>, int>);
  58         vector<string> getNextAvailableSet(vector<string>, vector<string>&);
  59         vector<string> getRestSet(vector<string>, vector<string>);
  60         bool isSubset(vector<string>, vector<string>);
  61         int findSpot(string);
  62         int buildConcensusTree(vector<string>);
  63
  64 };
  65
  66 #endif
  67