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#ifndef BOOTSTRAPSHAREDCOMMAND_H
#define BOOTSTRAPSHAREDCOMMAND_H
/*
* bootstrapsharedcommand.h
* Mothur
*
* Created by Sarah Westcott on 4/16/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "sharedordervector.h"
#include "inputdata.h"
#include "groupmap.h"
#include "validcalculator.h"
#include "tree.h"
#include "treemap.h"
#include "sharedutilities.h"
#include "consensuscommand.h"
class BootSharedCommand : public Command {
public:
BootSharedCommand(string);
BootSharedCommand();
~BootSharedCommand();
vector<string> setParameters();
string getCommandName() { return "bootstrap.shared"; }
string getCommandCategory() { return "Hidden"; }
string getHelpString();
string getCitation() { return "no citation"; }
string getDescription() { return "bootstrap.shared"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
int createTree(ostream*, Tree*);
void printSims();
int process(SharedOrderVector*);
SharedUtil* util;
TreeMap* tmap;
Tree* t;
Tree* tempTree;
ConcensusCommand* consensus;
vector< vector<Tree*> > trees; //a vector of trees for each calculator chosen
vector<Calculator*> treeCalculators;
vector<ofstream*> out;
vector< vector<float> > simMatrix;
map<int, int> index; //maps row in simMatrix to vector index in the tree
InputData* input;
ValidCalculators* validCalculator;
SharedOrderVector* order;
vector<SharedRAbundVector*> lookup;
bool abort, allLines;
set<string> labels; //holds labels to be used
string outputFile, calc, groups, label, outputDir, sharedfile;
int numGroups, iters;
vector<string> Estimators, Groups, outputNames; //holds estimators to be used
};
#endif
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