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();
  28                 ~UnifracWeightedCommand() { if (abort == false) {  delete weighted; delete util; } }
  29                 vector<string> getRequiredParameters();
  30                 vector<string> getValidParameters();
  31                 vector<string> getRequiredFiles();
  32                 map<string, vector<string> > getOutputFiles() { return outputTypes; }
  33                 int execute();
  34                 void help();
  35
  36         private:
  37                 struct linePair {
  38                         int start;
  39                         int num;
  40                         linePair(int i, int j) : start(i), num(j) {}
  41                 };
  42                 vector<linePair> lines;
  43
  44                 GlobalData* globaldata;
  45                 SharedUtil* util;
  46                 FileOutput* output;
  47                 vector<Tree*> T;           //user trees
  48                 vector<double> utreeScores;  //user tree unweighted scores
  49                 vector<double> WScoreSig;  //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
  50                 vector<string> groupComb; // AB. AC, BC...
  51                 TreeMap* tmap;
  52                 Weighted* weighted;
  53                 string sumFile, outputDir;
  54                 int iters, numGroups, numComp, counter;
  55                 EstOutput userData;                     //weighted score info for user tree
  56                 EstOutput randomData;           //weighted score info for random trees
  57                 vector< vector<double> > rScores;  //vector<weighted scores for random trees.> each group comb has an entry
  58                 vector< vector<double> > uScores;  //vector<weighted scores for user trees.> each group comb has an entry
  59                 vector< map<float, float> > rScoreFreq;  //map <weighted score, number of random trees with that score.> -vector entry for each combination.
  60                 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
  61                 map<float, float>  validScores;  //map contains scores from random
  62
  63                 bool abort, phylip, random;
  64                 string groups, itersString, outputForm;
  65                 vector<string> Groups, outputNames; //holds groups to be used
  66                 map<string, vector<string> > outputTypes;
  67                 int processors;
  68
  69
  70                 ofstream outSum;
  71
  72                 void printWSummaryFile();
  73                 void printWeightedFile();
  74                 void createPhylipFile();
  75                 //void removeValidScoresDuplicates();
  76                 int findIndex(float, int);
  77                 void calculateFreqsCumuls();
  78                 int createProcesses(Tree*,  vector< vector<string> >,  vector< vector<double> >&);
  79                 int driver(Tree*, vector< vector<string> >, int, int,  vector< vector<double> >&);
  80
  81 };
  82
  83
  84
  85 #endif