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