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#ifndef Mothur_classifytreecommand_h
#define Mothur_classifytreecommand_h
//
// classifytreecommand.h
// Mothur
//
// Created by Sarah Westcott on 2/20/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "command.hpp"
#include "readtree.h"
#include "treemap.h"
#include "counttable.h"
class ClassifyTreeCommand : public Command {
public:
ClassifyTreeCommand(string);
ClassifyTreeCommand();
~ClassifyTreeCommand(){}
vector<string> setParameters();
string getCommandName() { return "classify.tree"; }
string getCommandCategory() { return "Phylotype Analysis"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Classify.tree"; }
string getDescription() { return "Find the consensus taxonomy for the descendant of each tree node"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string treefile, taxonomyfile, groupfile, namefile, countfile, outputDir;
bool abort;
vector<string> outputNames;
int numUniquesInName, cutoff;
map<string, string> nameMap;
map<string, int> nameCount;
map<string, string> taxMap;
CountTable* ct;
int getClassifications(Tree*&);
map<string, set<string> > getDescendantList(Tree*&, int, map<int, map<string, set<string> > >);
string getTaxonomy(set<string>, int&);
};
#endif
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