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 "validcalculator.h"
  18 #include "tree.h"
  19 #include "treemap.h"
  20 #include "sharedutilities.h"
  21 #include "consensuscommand.h"
  22
  23 class BootSharedCommand : public Command {
  24
  25 public:
  26         BootSharedCommand(string);
  27         BootSharedCommand();
  28         ~BootSharedCommand();
  29
  30         vector<string> setParameters();
  31         string getCommandName()                 { return "bootstrap.shared";    }
  32         string getCommandCategory()             { return "Hidden";                              }
  33         string getHelpString();
  34         string getCitation() { return "no citation"; }
  35
  36
  37         int execute();
  38         void help() { m->mothurOut(getHelpString()); }
  39
  40 private:
  41         int createTree(ostream*, Tree*);
  42         void printSims();
  43         int process(SharedOrderVector*);
  44
  45         SharedUtil* util;
  46         TreeMap* tmap;
  47         Tree* t;
  48         Tree* tempTree;
  49         ConcensusCommand* consensus;
  50         vector< vector<Tree*> > trees;  //a vector of trees for each calculator chosen
  51         vector<Calculator*> treeCalculators;
  52         vector<ofstream*> out;
  53         vector< vector<float> > simMatrix;
  54         map<int, int> index;  //maps row in simMatrix to vector index in the tree
  55         InputData* input;
  56         ValidCalculators* validCalculator;
  57         SharedOrderVector* order;
  58         vector<SharedRAbundVector*> lookup;
  59
  60         bool abort, allLines;
  61         set<string> labels; //holds labels to be used
  62         string outputFile, calc, groups, label, outputDir, sharedfile;
  63         int numGroups, iters;
  64         vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
  65 };
  66
  67
  68 #endif
  69
  70