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 class GlobalData;
  21
  22 class UnifracUnweightedCommand : public Command {
  23
  24         public:
  25                 UnifracUnweightedCommand(string);
  26                 UnifracUnweightedCommand();
  27                 ~UnifracUnweightedCommand() { globaldata->Groups.clear();  if (abort == false) { delete unweighted; delete util; } }
  28                 vector<string> getRequiredParameters();
  29                 vector<string> getValidParameters();
  30                 vector<string> getRequiredFiles();
  31                 map<string, vector<string> > getOutputFiles() { return outputTypes; }
  32                 int execute();
  33                 void help();
  34
  35         private:
  36                 GlobalData* globaldata;
  37                 SharedUtil* util;
  38                 FileOutput* output;
  39                 vector<Tree*> T;           //user trees
  40                 TreeMap* tmap;
  41                 Unweighted* unweighted;
  42                 string sumFile, allGroups;
  43                 vector<string> groupComb; // AB. AC, BC...
  44                 int iters, numGroups, numComp, counter, processors;
  45                 EstOutput userData;                     //unweighted score info for user tree
  46                 EstOutput randomData;           //unweighted score info for random trees
  47                 vector< vector<float> > utreeScores; //scores for users trees for each comb.
  48                 vector< vector<float> > UWScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or higher.
  49                 map<float, float>  validScores;  //map contains scores from random
  50                 vector< map<float, float> > rscoreFreq;  //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
  51                 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.
  52
  53                 bool abort, phylip, random, includeRoot;
  54                 string groups, itersString, outputDir, outputForm;
  55                 vector<string> Groups, outputNames; //holds groups to be used
  56                 map<string, vector<string> > outputTypes;
  57
  58                 ofstream outSum, out;
  59                 ifstream inFile;
  60
  61                 void printUWSummaryFile(int);
  62                 void printUnweightedFile();
  63                 void createPhylipFile(int);
  64
  65
  66 };
  67
  68 #endif