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
  19
  20 class GlobalData;
  21
  22 class ParsimonyCommand : public Command {
  23
  24         public:
  25                 ParsimonyCommand();
  26                 ~ParsimonyCommand() { delete pars; delete util; delete output; }
  27                 int execute();
  28
  29         private:
  30                 GlobalData* globaldata;
  31                 SharedUtil* util;
  32                 FileOutput* output;
  33                 vector<Tree*> T;           //user trees
  34                 Tree* randT;  //random tree
  35                 Tree* copyUserTree;
  36                 TreeMap* tmap;
  37                 TreeMap* savetmap;
  38                 Parsimony* pars;
  39                 vector<string> groupComb; // AB. AC, BC...
  40                 string sumFile, randomtree, allGroups;
  41                 int iters, numGroups, numComp, counter;
  42                 vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
  43                 vector< vector<float> > userTreeScores; //scores for users trees for each comb.
  44                 vector< vector<float> > UScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
  45                 EstOutput userData;                     //pscore info for user tree
  46                 EstOutput randomData;           //pscore info for random trees
  47                 map<int, double>  validScores;  //map contains scores from both user and random
  48                 vector< map<int, double> > rscoreFreq;  //map <pscore, number of random trees with that score.> -vector entry for each combination.
  49                 vector< map<int, double> > uscoreFreq;  //map <pscore, number of user trees with that score.> -vector entry for each combination.
  50                 vector< map<int, double> > rCumul;  //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
  51                 vector< map<int, double> > uCumul;  //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
  52                 map<int, double>::iterator it;
  53                 map<int, double>::iterator it2;
  54
  55                 ofstream out, outSum;
  56                 ifstream inFile;
  57
  58                 void printParsimonyFile();
  59                 void printUSummaryFile();
  60                 void getUserInput();
  61
  62 };
  63
  64
  65 #endif