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(string);
  26                 ~ParsimonyCommand() { delete pars; delete util; delete output; }
  27                 int execute();
  28                 void help();
  29
  30         private:
  31                 GlobalData* globaldata;
  32                 SharedUtil* util;
  33                 FileOutput* output;
  34                 vector<Tree*> T;           //user trees
  35                 Tree* randT;  //random tree
  36                 Tree* copyUserTree;
  37                 TreeMap* tmap;
  38                 TreeMap* savetmap;
  39                 Parsimony* pars;
  40                 vector<string> groupComb; // AB. AC, BC...
  41                 string sumFile, randomtree, allGroups;
  42                 int iters, numGroups, numComp, counter;
  43                 vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
  44                 vector< vector<float> > userTreeScores; //scores for users trees for each comb.
  45                 vector< vector<float> > UScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
  46                 EstOutput userData;                     //pscore info for user tree
  47                 EstOutput randomData;           //pscore info for random trees
  48                 map<int, double>  validScores;  //map contains scores from both user and random
  49                 vector< map<int, double> > rscoreFreq;  //map <pscore, number of random trees with that score.> -vector entry for each combination.
  50                 vector< map<int, double> > uscoreFreq;  //map <pscore, number of user trees with that score.> -vector entry for each combination.
  51                 vector< map<int, double> > rCumul;  //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
  52                 vector< map<int, double> > uCumul;  //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
  53                 map<int, double>::iterator it;
  54                 map<int, double>::iterator it2;
  55
  56                 ofstream out, outSum;
  57                 ifstream inFile;
  58
  59                 OptionParser* parser;
  60                 map<string, string> parameters;
  61                 map<string, string>::iterator it4;
  62                 bool abort;
  63                 string groups, itersString;
  64                 vector<string> Groups; //holds groups to be used
  65
  66                 void printParsimonyFile();
  67                 void printUSummaryFile();
  68                 void getUserInput();
  69
  70 };
  71
  72
  73 #endif