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"
17 #include "validcalculator.h"
20 #include "sharedutilities.h"
21 #include "consensuscommand.h"
23 class BootSharedCommand : public Command {
26 BootSharedCommand(string);
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 string getDescription() { return "bootstrap.shared"; }
39 void help() { m->mothurOut(getHelpString()); }
42 int createTree(ostream*, Tree*);
44 int process(SharedOrderVector*);
50 ConcensusCommand* consensus;
51 vector< vector<Tree*> > trees; //a vector of trees for each calculator chosen
52 vector<Calculator*> treeCalculators;
53 vector<ofstream*> out;
54 vector< vector<float> > simMatrix;
55 map<int, int> index; //maps row in simMatrix to vector index in the tree
57 ValidCalculators* validCalculator;
58 SharedOrderVector* order;
59 vector<SharedRAbundVector*> lookup;
62 set<string> labels; //holds labels to be used
63 string outputFile, calc, groups, label, outputDir, sharedfile;
65 vector<string> Estimators, Groups, outputNames; //holds estimators to be used