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         ~BootSharedCommand();
  32         vector<string> getRequiredParameters();
  33         vector<string> getValidParameters();
  34         vector<string> getRequiredFiles();
  35         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  36         int execute();
  37         void help();
  38
  39 private:
  40         int createTree(ostream*, Tree*);
  41         void printSims();
  42         int process(SharedOrderVector*);
  43
  44
  45         GlobalData* globaldata;
  46         SharedUtil* util;
  47         ReadOTUFile* read;
  48         TreeMap* tmap;
  49         Tree* t;
  50         Tree* tempTree;
  51         ConcensusCommand* consensus;
  52         vector< vector<Tree*> > trees;  //a vector of trees for each calculator chosen
  53         vector<Calculator*> treeCalculators;
  54         vector<ofstream*> out;
  55         vector< vector<float> > simMatrix;
  56         map<int, int> index;  //maps row in simMatrix to vector index in the tree
  57         InputData* input;
  58         ValidCalculators* validCalculator;
  59         SharedOrderVector* order;
  60         vector<SharedRAbundVector*> lookup;
  61
  62         bool abort, allLines;
  63         set<string> labels; //holds labels to be used
  64         string outputFile, calc, groups, label, outputDir;
  65         int numGroups, iters;
  66         vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
  67         map< string, vector<string> > outputTypes;
  68
  69 };
  70
  71
  72 #endif
  73
  74