unifracunweightedcommand.h

   1 #ifndef UNIFRACUNWEIGHTEDCOMMAND_H
   2 #define UNIFRACUNWEIGHTEDCOMMAND_H
   3
   4 /*
   5  *  unifracunweightedcommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 2/9/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 #include <iostream>
  14 #include <fstream>
  15 #include <vector>
  16 #include <map>
  17 #include <cmath>
  18 #include "command.hpp"
  19 #include "unweighted.h"
  20 #include "treemap.h"
  21
  22 using namespace std;
  23
  24 class GlobalData;
  25
  26 class UnifracUnweightedCommand : public Command {
  27
  28         public:
  29                 UnifracUnweightedCommand();
  30                 ~UnifracUnweightedCommand() { delete unweighted; }
  31                 int execute();
  32
  33         private:
  34                 GlobalData* globaldata;
  35                 vector<Tree*> T;           //user trees
  36                 vector<float> utreeScores;  //user tree unweighted scores
  37                 vector<float> UWScoreSig;  //tree unweighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
  38                 Tree* randT;  //random tree
  39                 TreeMap* tmap;
  40                 Unweighted* unweighted;
  41                 string sumFile, distFile, unweightedFile;
  42                 int iters;
  43                 EstOutput userData;                     //unweighted score info for user tree
  44                 EstOutput randomData;           //unweighted score info for random trees
  45                 map<float, float> validScores;  //contains scores from both user and random
  46                 map<float, float> rscoreFreq;  //unweighted score, number of random trees with that score.
  47                 map<float, float> uscoreFreq;  //unweighted, number of user trees with that score.
  48                 map<float, float> totalrscoreFreq;  //unweighted score, number of random trees with that score.
  49                 map<float, float> rCumul;               //unweighted score, cumulative percentage of number of random trees with that score or higher.
  50                 map<float, float> uCumul;  //unweighted, cumulative percentage of number of user trees with that score or higher .
  51                 map<float, float>::iterator it;
  52                 map<float, float>::iterator it2;
  53
  54                 ofstream outSum, outDist, out;
  55
  56                 void printUWSummaryFile();
  57                 void printUnweightedFile();
  58                 void saveRandomScores();
  59
  60 };
  61
  62
  63
  64 #endif