unifracweightedcommand.h

   1 #ifndef UNIFRACWEIGHTEDCOMMAND_H
   2 #define UNIFRACWEIGHTEDCOMMAND_H
   3
   4 /*
   5  *  unifracweightedcommand.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 "weighted.h"
  20 #include "treemap.h"
  21
  22 using namespace std;
  23
  24 class GlobalData;
  25
  26 class UnifracWeightedCommand : public Command {
  27
  28         public:
  29                 UnifracWeightedCommand();
  30                 ~UnifracWeightedCommand() { delete weighted; }
  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> WScoreSig;  //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
  38                 vector<string> groupComb; // AB. AC, BC...
  39                 Tree* randT;  //random tree
  40                 TreeMap* tmap;
  41                 Weighted* weighted;
  42                 string weightedFile, sumFile, distFile;
  43                 int iters, numGroups, numComp;
  44                 EstOutput userData;                     //weighted score info for user tree
  45                 EstOutput randomData;           //weighted score info for random trees
  46                 vector< map<float, float> > validScores;  //vector<contains scores from both user and random> each group comb has an entry
  47                 vector< map<float, float> > rscoreFreq;  //vector<weighted score, number of random trees with that score.> each group comb has an entry
  48                 vector< map<float, float> > uscoreFreq;  //vector<weighted, number of user trees with that score.> each group comb has an entry
  49                 vector< map<float, float> > totalrscoreFreq;  //vector<weighted score, number of random trees with that score.> each group comb has an entry
  50                 vector< map<float, float> > rCumul;  //vector<weighted score, number of random trees with that score or higher.> each group comb has an entry
  51                 vector< map<float, float> > uCumul;  //vector<weighted, cumulative percentage of number of user trees with that score or higher.> each group comb has an entry
  52                 map<float, float>::iterator it;
  53                 map<float, float>::iterator it2;
  54
  55                 ofstream outSum, outDist, out;
  56
  57                 void printWSummaryFile();
  58                 void printWeightedFile();
  59                 void saveRandomScores();
  60 };
  61
  62
  63
  64 #endif