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                 struct linePair {
  33                         int start;
  34                         int num;
  35                         linePair(int i, int j) : start(i), num(j) {}
  36                 };
  37                 vector<linePair> lines;
  38
  39                 GlobalData* globaldata;
  40                 SharedUtil* util;
  41                 FileOutput* output;
  42                 vector<Tree*> T;           //user trees
  43                 vector<double> utreeScores;  //user tree unweighted scores
  44                 vector<double> WScoreSig;  //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
  45                 vector<string> groupComb; // AB. AC, BC...
  46                 TreeMap* tmap;
  47                 Weighted* weighted;
  48                 string sumFile, outputDir;
  49                 int iters, numGroups, numComp, counter;
  50                 EstOutput userData;                     //weighted score info for user tree
  51                 EstOutput randomData;           //weighted score info for random trees
  52                 vector< vector<double> > rScores;  //vector<weighted scores for random trees.> each group comb has an entry
  53                 vector< vector<double> > uScores;  //vector<weighted scores for user trees.> each group comb has an entry
  54                 vector< map<float, float> > rScoreFreq;  //map <weighted score, number of random trees with that score.> -vector entry for each combination.
  55                 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
  56                 map<float, float>  validScores;  //map contains scores from random
  57
  58                 bool abort, phylip, random;
  59                 string groups, itersString;
  60                 vector<string> Groups, outputNames; //holds groups to be used
  61                 int processors;
  62
  63
  64                 ofstream outSum;
  65
  66                 void printWSummaryFile();
  67                 void printWeightedFile();
  68                 void createPhylipFile();
  69                 //void removeValidScoresDuplicates();
  70                 int findIndex(float, int);
  71                 void calculateFreqsCumuls();
  72                 int createProcesses(Tree*,  vector< vector<string> >, vector<double>&, vector< vector<double> >&);
  73                 int driver(Tree*, vector< vector<string> >, int, int, vector<double>&, vector< vector<double> >&);
  74
  75 };
  76
  77
  78
  79 #endif