bootstrapsharedcommand.h

   1 #ifndef BOOTSTRAPSHAREDCOMMAND_H
   2 #define BOOTSTRAPSHAREDCOMMAND_H
   3
   4 /*
   5  *  bootstrapsharedcommand.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 4/16/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 #include "command.hpp"
  14 #include "sharedordervector.h"
  15 #include "inputdata.h"
  16 #include "groupmap.h"
  17 #include "readotu.h"
  18 #include "validcalculator.h"
  19 #include "tree.h"
  20 #include "treemap.h"
  21 #include "sharedutilities.h"
  22 #include "consensuscommand.h"
  23
  24 class GlobalData;
  25
  26 class BootSharedCommand : public Command {
  27
  28 public:
  29         BootSharedCommand(string);
  30         ~BootSharedCommand();
  31         int execute();
  32         void help();
  33
  34 private:
  35         void createTree(ostream*, Tree*);
  36         void printSims();
  37         void process(SharedOrderVector*);
  38
  39
  40         GlobalData* globaldata;
  41         SharedUtil* util;
  42         ReadOTUFile* read;
  43         TreeMap* tmap;
  44         Tree* t;
  45         Tree* tempTree;
  46         ConcensusCommand* consensus;
  47         vector< vector<Tree*> > trees;  //a vector of trees for each calculator chosen
  48         vector<Calculator*> treeCalculators;
  49         vector<ofstream*> out;
  50         vector< vector<float> > simMatrix;
  51         map<int, int> index;  //maps row in simMatrix to vector index in the tree
  52         InputData* input;
  53         ValidCalculators* validCalculator;
  54         SharedOrderVector* order;
  55         vector<SharedRAbundVector*> lookup;
  56
  57         bool abort, allLines;
  58         set<string> labels; //holds labels to be used
  59         string outputFile, calc, groups, label, outputDir;
  60         int numGroups, iters;
  61         vector<string>  Estimators, Groups; //holds estimators to be used
  62
  63 };
  64
  65
  66 #endif
  67
  68