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//
// getdistscommand.h
// Mothur
//
// Created by Sarah Westcott on 1/28/13.
// Copyright (c) 2013 Schloss Lab. All rights reserved.
//
#ifndef Mothur_getdistscommand_h
#define Mothur_getdistscommand_h
#include "command.hpp"
class GetDistsCommand : public Command {
public:
GetDistsCommand(string);
~GetDistsCommand(){}
vector<string> setParameters();
string getCommandName() { return "get.dists"; }
string getCommandCategory() { return "General"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.dists"; }
string getDescription() { return "gets distances from a phylip or column file related to groups or sequences listed in an accnos file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
unordered_set<string> names;
string accnosfile, phylipfile, columnfile;
bool abort;
vector<string> outputNames;
int readPhylip();
int readColumn();
};
#endif
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