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 "counttable.h"
  16 #include "sharedutilities.h"
  17 #include "fileoutput.h"
  18 #include "readtree.h"
  19
  20 class UnifracUnweightedCommand : public Command {
  21
  22         public:
  23                 UnifracUnweightedCommand(string);
  24                 UnifracUnweightedCommand();
  25                 ~UnifracUnweightedCommand() {}
  26
  27                 vector<string> setParameters();
  28                 string getCommandName()                 { return "unifrac.unweighted";          }
  29                 string getCommandCategory()             { return "Hypothesis Testing";          }
  30
  31         string getHelpString();
  32     string getOutputPattern(string);
  33                 string getCitation() { return "Lozupone C, Knight R (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-35. \nhttp://www.mothur.org/wiki/Unifrac.unweighted"; }
  34                 string getDescription()         { return "generic tests that describes whether two or more communities have the same structure"; }
  35
  36                 int execute();
  37                 void help() { m->mothurOut(getHelpString()); }
  38
  39
  40         private:
  41                 FileOutput* output;
  42                 vector<Tree*> T;           //user trees
  43                 CountTable* ct;
  44                 string sumFile, allGroups;
  45                 vector<string> groupComb; // AB. AC, BC...
  46                 int iters, numGroups, numComp, counter, processors, subsampleSize, subsampleIters;
  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, consensus, subsample;
  54                 string groups, itersString, outputDir, outputForm, treefile, groupfile, namefile, countfile;
  55                 vector<string> Groups, outputNames; //holds groups to be used
  56
  57                 ofstream outSum, out;
  58                 ifstream inFile;
  59
  60         int runRandomCalcs(Tree*, vector<double>);
  61                 void printUWSummaryFile(int);
  62                 void printUnweightedFile();
  63                 void createPhylipFile(int);
  64         vector<Tree*> buildTrees(vector< vector<double> >&, int, CountTable&);
  65         int getConsensusTrees(vector< vector<double> >&, int);
  66         int getAverageSTDMatrices(vector< vector<double> >&, int);
  67
  68 };
  69
  70 #endif