parsimonycommand.h

   1 #ifndef PARSIMONYCOMMAND_H
   2 #define PARSIMONYCOMMAND_H
   3 /*
   4  *  parsimonycommand.h
   5  *  Mothur
   6  *
   7  *  Created by Sarah Westcott on 1/26/09.
   8  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   9  *
  10  */
  11
  12 #include "command.hpp"
  13 #include "parsimony.h"
  14 #include "treemap.h"
  15 #include "progress.hpp"
  16 #include "sharedutilities.h"
  17 #include "fileoutput.h"
  18 #include "readtree.h"
  19
  20
  21 class ParsimonyCommand : public Command {
  22
  23 public:
  24         ParsimonyCommand(string);
  25         ParsimonyCommand();
  26         ~ParsimonyCommand(){}
  27
  28         vector<string> setParameters();
  29         string getCommandName()                 { return "parsimony";                           }
  30         string getCommandCategory()             { return "Hypothesis Testing";          }
  31         string getHelpString();
  32
  33         int execute();
  34         void help() { m->mothurOut(getHelpString()); }
  35
  36 private:
  37         ReadTree* read;
  38         SharedUtil* util;
  39         FileOutput* output;
  40         vector<Tree*> T;           //user trees
  41         Tree* randT;  //random tree
  42         Tree* copyUserTree;
  43         TreeMap* tmap;
  44         TreeMap* savetmap;
  45         Parsimony* pars;
  46         vector<string> groupComb; // AB. AC, BC...
  47         string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile;
  48         int iters, numGroups, numComp, counter, processors, numUniquesInName;
  49         vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
  50         vector< vector<float> > userTreeScores; //scores for users trees for each comb.
  51         vector< vector<float> > UScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
  52         EstOutput userData;                     //pscore info for user tree
  53         EstOutput randomData;           //pscore info for random trees
  54         map<int, double>  validScores;  //map contains scores from both user and random
  55         vector< map<int, double> > rscoreFreq;  //map <pscore, number of random trees with that score.> -vector entry for each combination.
  56         vector< map<int, double> > uscoreFreq;  //map <pscore, number of user trees with that score.> -vector entry for each combination.
  57         vector< map<int, double> > rCumul;  //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
  58         vector< map<int, double> > uCumul;  //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
  59
  60         ofstream outSum;
  61         bool abort;
  62         string groups, itersString;
  63         vector<string> Groups, outputNames; //holds groups to be used
  64         map<string, string> nameMap;
  65
  66         void printParsimonyFile();
  67         int printUSummaryFile();
  68         void getUserInput();
  69         int readNamesFile();
  70
  71 };
  72
  73
  74 #endif