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 "command.hpp"
  14 #include "weighted.h"
  15 #include "treemap.h"
  16 #include "progress.hpp"
  17
  18 using namespace std;
  19
  20 class GlobalData;
  21
  22 class UnifracWeightedCommand : public Command {
  23
  24         public:
  25                 UnifracWeightedCommand();
  26                 ~UnifracWeightedCommand() { delete weighted; }
  27                 int execute();
  28
  29         private:
  30                 GlobalData* globaldata;
  31                 vector<Tree*> T;           //user trees
  32                 vector<double> utreeScores;  //user tree unweighted scores
  33                 vector<double> WScoreSig;  //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
  34                 vector<string> groupComb; // AB. AC, BC...
  35                 Tree* randT;  //random tree
  36                 TreeMap* tmap;
  37                 Weighted* weighted;
  38                 string weightedFile, weightedFileout, sumFile;
  39                 int iters, numGroups, numComp, counter;
  40                 EstOutput userData;                     //weighted score info for user tree
  41                 EstOutput randomData;           //weighted score info for random trees
  42                 vector< vector<double> > rScores;  //vector<weighted scores for random trees.> each group comb has an entry
  43                 vector< vector<double> > uScores;  //vector<weighted scores for user trees.> each group comb has an entry
  44                 vector< map<float, float> > rScoreFreq;  //map <weighted score, number of random trees with that score.> -vector entry for each combination.
  45                 vector< map<float, float> > rCumul;  //map <weighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each c
  46                 map<float, float>  validScores;  //map contains scores from random
  47                 map<float, float>::iterator it2;
  48                 map<float, float>::iterator it;
  49
  50                 ofstream outSum, out;
  51                 ifstream inFile;
  52
  53                 void printWSummaryFile();
  54                 void printWeightedFile();
  55                 //void removeValidScoresDuplicates();
  56                 int findIndex(float, int);
  57                 void setGroups();
  58                 void calculateFreqsCumuls();
  59                 void initFile(string);
  60                 void output(vector<double>);
  61                 void resetFile();
  62
  63 };
  64
  65
  66
  67 #endif