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 "command.hpp"
  14 #include "unweighted.h"
  15 #include "treemap.h"
  16
  17 using namespace std;
  18
  19 class GlobalData;
  20
  21 class UnifracUnweightedCommand : public Command {
  22
  23         public:
  24                 UnifracUnweightedCommand();
  25                 ~UnifracUnweightedCommand() { delete unweighted; }
  26                 int execute();
  27
  28         private:
  29                 GlobalData* globaldata;
  30                 vector<Tree*> T;           //user trees
  31                 vector<float> utreeScores;  //user tree unweighted scores
  32                 vector<float> UWScoreSig;  //tree unweighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
  33                 Tree* randT;  //random tree
  34                 TreeMap* tmap;
  35                 Unweighted* unweighted;
  36                 string sumFile, distFile, unweightedFile;
  37                 int iters;
  38                 EstOutput userData;                     //unweighted score info for user tree
  39                 EstOutput randomData;           //unweighted score info for random trees
  40                 map<float, float> validScores;  //contains scores from both user and random
  41                 map<float, float> rscoreFreq;  //unweighted score, number of random trees with that score.
  42                 map<float, float> uscoreFreq;  //unweighted, number of user trees with that score.
  43                 map<float, float> totalrscoreFreq;  //unweighted score, number of random trees with that score.
  44                 map<float, float> rCumul;               //unweighted score, cumulative percentage of number of random trees with that score or higher.
  45                 map<float, float> uCumul;  //unweighted, cumulative percentage of number of user trees with that score or higher .
  46                 map<float, float>::iterator it;
  47                 map<float, float>::iterator it2;
  48
  49                 ofstream outSum, outDist, out;
  50
  51                 void printUWSummaryFile();
  52                 void printUnweightedFile();
  53                 void saveRandomScores();
  54
  55 };
  56
  57
  58
  59 #endif