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
  16 using namespace std;
  17
  18 class GlobalData;
  19
  20 class ParsimonyCommand : public Command {
  21
  22         public:
  23                 ParsimonyCommand();
  24                 ~ParsimonyCommand() { delete pars; }
  25                 int execute();
  26
  27         private:
  28                 GlobalData* globaldata;
  29                 vector<Tree*> T;           //user trees
  30                 Tree* randT;  //random tree
  31                 Tree* copyUserTree;
  32                 TreeMap* tmap;
  33                 TreeMap* savetmap;
  34                 Parsimony* pars;
  35                 vector<string> groupComb; // AB. AC, BC...
  36                 string parsFile, sumFile, randomtree;
  37                 int iters, numGroups, numComp;
  38                 vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
  39                 vector< vector<float> > userTreeScores; //scores for users trees for each comb.
  40                 vector< vector<float> > UScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
  41                 EstOutput userData;                     //pscore info for user tree
  42                 EstOutput randomData;           //pscore info for random trees
  43                 vector< map<int, double> > validScores;  //map contains scores from both user and random
  44                 vector< map<int, double> > rscoreFreq;  //map <pscore, number of random trees with that score.> -vector entry for each combination.
  45                 vector< map<int, double> > uscoreFreq;  //map <pscore, number of user trees with that score.> -vector entry for each combination.
  46                 vector< map<int, double> > rCumul;  //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
  47                 vector< map<int, double> > uCumul;  //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
  48                 map<int, double>::iterator it;
  49                 map<int, double>::iterator it2;
  50
  51                 ofstream out, outSum;
  52
  53                 void printParsimonyFile();
  54                 void printUSummaryFile();
  55                 void getUserInput();
  56                 void setGroups();
  57
  58 };
  59
  60
  61 #endif