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 "sharedlistvector.h"
  16 #include "inputdata.h"
  17 #include "groupmap.h"
  18 #include "readotu.h"
  19 #include "validcalculator.h"
  20 #include "tree.h"
  21 #include "treemap.h"
  22 #include "sharedutilities.h"
  23
  24 class GlobalData;
  25
  26 class BootSharedCommand : public Command {
  27
  28 public:
  29         BootSharedCommand();
  30         ~BootSharedCommand();
  31         int execute();
  32
  33 private:
  34         void createTree(ostream*);
  35         void printSims();
  36
  37         GlobalData* globaldata;
  38         SharedUtil* util;
  39         ReadOTUFile* read;
  40         TreeMap* tmap;
  41         Tree* t;
  42         vector<Calculator*> treeCalculators;
  43         vector<ofstream*> out;
  44         vector< vector<float> > simMatrix;
  45         map<int, int> index;  //maps row in simMatrix to vector index in the tree
  46         InputData* input;
  47         ValidCalculators* validCalculator;
  48         SharedListVector* SharedList;
  49         SharedOrderVector* order;
  50         vector<SharedRAbundVector*> lookup;
  51         string format, outputFile;
  52         int numGroups, iters;
  53
  54 };
  55
  56
  57 #endif
  58
  59