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 #include "sharedutilities.h"
  18 #include "fileoutput.h"
  19
  20
  21 class GlobalData;
  22
  23 class UnifracWeightedCommand : public Command {
  24
  25         public:
  26                 UnifracWeightedCommand(string);
  27                 ~UnifracWeightedCommand() { if (abort == false) {  delete weighted; delete util; } }
  28                 int execute();
  29                 void help();
  30
  31         private:
  32                 GlobalData* globaldata;
  33                 SharedUtil* util;
  34                 FileOutput* output;
  35                 vector<Tree*> T;           //user trees
  36                 vector<double> utreeScores;  //user tree unweighted scores
  37                 vector<double> 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 sumFile, outputDir;
  43                 int iters, numGroups, numComp, counter;
  44                 EstOutput userData;                     //weighted score info for user tree
  45                 EstOutput randomData;           //weighted score info for random trees
  46                 vector< vector<double> > rScores;  //vector<weighted scores for random trees.> each group comb has an entry
  47                 vector< vector<double> > uScores;  //vector<weighted scores for user trees.> each group comb has an entry
  48                 vector< map<float, float> > rScoreFreq;  //map <weighted score, number of random trees with that score.> -vector entry for each combination.
  49                 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
  50                 map<float, float>  validScores;  //map contains scores from random
  51
  52                 bool abort, phylip, random;
  53                 string groups, itersString;
  54                 vector<string> Groups, outputNames; //holds groups to be used
  55
  56
  57                 ofstream outSum;
  58
  59                 void printWSummaryFile();
  60                 void printWeightedFile();
  61                 void createPhylipFile();
  62                 //void removeValidScoresDuplicates();
  63                 int findIndex(float, int);
  64                 void calculateFreqsCumuls();
  65
  66 };
  67
  68
  69
  70 #endif