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#ifndef GETLINEAGECOMMAND_H
#define GETLINEAGECOMMAND_H
/*
* getlineagecommand.h
* Mothur
*
* Created by westcott on 9/24/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "sharedrabundvectors.hpp"
#include "listvector.hpp"
#include "getseqscommand.h"
#include "getotuscommand.h"
#include "taxonomy.hpp"
class GetLineageCommand : public Command {
public:
GetLineageCommand(string);
~GetLineageCommand(){}
vector<string> setParameters();
string getCommandName() { return "get.lineage"; }
string getCommandCategory() { return "Phylotype Analysis"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Get.lineage"; }
string getDescription() { return "gets sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<string> outputNames, listOfTaxons;
string fastafile, namefile, groupfile, alignfile, countfile, listfile, taxfile, taxons, sharedfile, constaxonomy, label;
bool abort, dups;
string readTax();
string readConsTax();
int runGetOTUs(string);
int runGetSeqs(string);
};
#endif
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