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
  23 class GlobalData;
  24
  25 class BootSharedCommand : public Command {
  26
  27 public:
  28         BootSharedCommand(string);
  29         ~BootSharedCommand();
  30         int execute();
  31         void help();
  32
  33 private:
  34         void createTree(ostream*);
  35         void printSims();
  36         void process(SharedOrderVector*);
  37
  38
  39         GlobalData* globaldata;
  40         SharedUtil* util;
  41         ReadOTUFile* read;
  42         TreeMap* tmap;
  43         Tree* t;
  44         vector<Calculator*> treeCalculators;
  45         vector<ofstream*> out;
  46         vector< vector<float> > simMatrix;
  47         map<int, int> index;  //maps row in simMatrix to vector index in the tree
  48         InputData* input;
  49         ValidCalculators* validCalculator;
  50         SharedOrderVector* order;
  51         vector<SharedRAbundVector*> lookup;
  52         OptionParser* parser;
  53         map<string, string> parameters;
  54         map<string, string>::iterator it;
  55         bool abort, allLines;
  56         set<int> lines; //hold lines to be used
  57         set<string> labels; //holds labels to be used
  58         string outputFile, calc, groups, line, label;
  59         int numGroups, iters;
  60         vector<string>  Estimators, Groups; //holds estimators to be used
  61
  62 };
  63
  64
  65 #endif
  66
  67