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"
25 class BootSharedCommand : public Command {
28 BootSharedCommand(string);
34 void createTree(ostream*);
36 void process(SharedOrderVector*);
39 GlobalData* globaldata;
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
49 ValidCalculators* validCalculator;
50 SharedOrderVector* order;
51 vector<SharedRAbundVector*> lookup;
54 set<int> lines; //hold lines to be used
55 set<string> labels; //holds labels to be used
56 string outputFile, calc, groups, line, label;
58 vector<string> Estimators, Groups; //holds estimators to be used