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