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"; }
38 void help() { m->mothurOut(getHelpString()); }
41 int createTree(ostream*, Tree*);
43 int process(SharedOrderVector*);
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
56 ValidCalculators* validCalculator;
57 SharedOrderVector* order;
58 vector<SharedRAbundVector*> lookup;
61 set<string> labels; //holds labels to be used
62 string outputFile, calc, groups, label, outputDir, sharedfile;
64 vector<string> Estimators, Groups, outputNames; //holds estimators to be used