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 #include "sharedutilities.h"
  17 #include "fileoutput.h"
  18
  19
  20 using namespace std;
  21
  22 class GlobalData;
  23
  24 class UnifracUnweightedCommand : public Command {
  25
  26         public:
  27                 UnifracUnweightedCommand();
  28                 ~UnifracUnweightedCommand() { delete unweighted; delete util; }
  29                 int execute();
  30
  31         private:
  32                 GlobalData* globaldata;
  33                 SharedUtil* util;
  34                 FileOutput* output;
  35                 vector<Tree*> T;           //user trees
  36                 TreeMap* tmap;
  37                 Unweighted* unweighted;
  38                 string sumFile, allGroups;
  39                 vector<string> groupComb; // AB. AC, BC...
  40                 int iters, numGroups, numComp, counter;
  41                 EstOutput userData;                     //unweighted score info for user tree
  42                 EstOutput randomData;           //unweighted score info for random trees
  43                 vector< vector<float> > utreeScores; //scores for users trees for each comb.
  44                 vector< vector<float> > UWScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or higher.
  45                 map<float, float>  validScores;  //map contains scores from random
  46                 vector< map<float, float> > rscoreFreq;  //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
  47                 vector< map<float, float> > rCumul;  //map <unweighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each combination.
  48                 map<float, float>::iterator it2;
  49                 map<float, float>::iterator it;
  50
  51                 ofstream outSum, out;
  52                 ifstream inFile;
  53
  54                 void printUWSummaryFile();
  55                 void printUnweightedFile();
  56
  57
  58 };
  59
  60
  61
  62 #endif