1 #ifndef BOOTSTRAPSHAREDCOMMAND_H
2 #define BOOTSTRAPSHAREDCOMMAND_H
5 * bootstrapsharedcommand.h
8 * Created by Sarah Westcott on 4/16/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
13 #include "command.hpp"
14 #include "sharedordervector.h"
15 #include "inputdata.h"
18 #include "validcalculator.h"
21 #include "sharedutilities.h"
22 #include "consensuscommand.h"
26 class BootSharedCommand : public Command {
29 BootSharedCommand(string);
35 void createTree(ostream*, Tree*);
37 void process(SharedOrderVector*);
40 GlobalData* globaldata;
46 ConcensusCommand* consensus;
47 vector< vector<Tree*> > trees; //a vector of trees for each calculator chosen
48 vector<Calculator*> treeCalculators;
49 vector<ofstream*> out;
50 vector< vector<float> > simMatrix;
51 map<int, int> index; //maps row in simMatrix to vector index in the tree
53 ValidCalculators* validCalculator;
54 SharedOrderVector* order;
55 vector<SharedRAbundVector*> lookup;
58 set<int> lines; //hold lines to be used
59 set<string> labels; //holds labels to be used
60 string outputFile, calc, groups, line, label;
62 vector<string> Estimators, Groups; //holds estimators to be used