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//
// mergetaxsummarycommand.h
// Mothur
//
// Created by Sarah Westcott on 2/13/13.
// Copyright (c) 2013 Schloss Lab. All rights reserved.
//
#ifndef Mothur_mergetaxsummarycommand_h
#define Mothur_mergetaxsummarycommand_h
#include "mothur.h"
#include "command.hpp"
#include "phylosummary.h"
class MergeTaxSummaryCommand : public Command {
public:
MergeTaxSummaryCommand(string);
~MergeTaxSummaryCommand(){}
vector<string> setParameters();
string getCommandName() { return "merge.taxsummary"; }
string getCommandCategory() { return "Phylotype Analysis"; }
string getHelpString();
string getOutputPattern(string){ return ""; }
string getCitation() { return "http://www.mothur.org/wiki/Merge.taxsummary"; }
string getDescription() { return "merges tax summary files creating one file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<string> fileNames, outputNames;
string outputFileName;
int numInputFiles;
bool abort;
int addTaxToTree(vector<rawTaxNode>&, int, int, string, int, map<string, int>);
int assignRank(int index, vector<rawTaxNode>& tree);
int print(ofstream& out, vector<rawTaxNode>& tree, set<string> groups);
int print(int, ofstream& out, vector<rawTaxNode>& tree, set<string> groups);
};
#endif
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