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#ifndef SUBSAMPLECOMMAND_H
#define SUBSAMPLECOMMAND_H
/*
* subsamplecommand.h
* Mothur
*
* Created by westcott on 10/27/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "listvector.hpp"
#include "rabundvector.hpp"
#include "inputdata.h"
#include "sequence.hpp"
#include "counttable.h"
#include "treereader.h"
class SubSampleCommand : public Command {
public:
SubSampleCommand(string);
~SubSampleCommand() = default;
vector<string> setParameters();
string getCommandName() { return "sub.sample"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Sub.sample"; }
string getDescription() { return "get a sampling of sequences from a list, shared, rabund, sabund or fasta file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, pickedGroups, allLines, persample, withReplacement;
string listfile, groupfile, countfile, sharedfile, rabundfile, sabundfile, fastafile, namefile, taxonomyfile, treefile, constaxonomyfile;
set<string> labels; //holds labels to be used
string groups, label;
vector<string> Groups, outputNames;
int size;
//vector<string> names;
map<string, vector<string> > nameMap;
CountTable ct;
int getSubSampleShared();
int getSubSampleList();
void getSubSampleRabund();
void getSubSampleSabund();
int getSubSampleFasta();
int getSubSampleTree();
int processShared(SharedRAbundVectors*&);
int processRabund(RAbundVector*&, ofstream&);
int processSabund(SAbundVector*&, ofstream&);
int processList(ListVector*&, set<string>&);
vector<string> getNames();
vector<string> readNames();
int getTax(set<string>&);
};
#endif
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