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#ifndef COLLECTCOMMAND_H
#define COLLECTCOMMAND_H
/*
* collectcommand.h
* Dotur
*
* Created by Sarah Westcott on 1/2/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "ordervector.hpp"
#include "inputdata.h"
#include "collect.h"
#include "validcalculator.h"
/*The collect() command:
The collect command generates a collector's curve from the given file.
The collect command outputs a file for each estimator you choose to use. The collect command parameters are label, freq, single, abund.
No parameters are required.
The collect command should be in the following format: collect(label=yourLabel, freq=yourFreq, single=yourEstimators, abund=yourAbund).
example collect(label=unique-.01-.03, freq=10, single=collect-chao-ace-jack).
The default values for freq is 100, for abund is 10, and single are collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson.
The valid single estimators are: collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson.
The label parameter is used to analyze specific labels in your input. */
class CollectCommand : public Command {
public:
CollectCommand(string);
~CollectCommand(){}
vector<string> setParameters();
string getCommandName() { return "collect.single"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.single"; }
string getHelpString();
string getOutputPattern(string);
string getDescription() { return "generates collector's curves using calculators, that describe the richness, diversity, and other features of individual samples"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<Display*> cDisplays;
int abund, size, alpha;
float freq;
vector<string> outputNames, groups;
bool abort, allLines;
set<string> labels; //holds labels to be used
string label, calc, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
vector<string> Estimators;
vector<string> inputFileNames;
vector<string> parseSharedFile(string);
void fillCDisplays(map<string, string>);
};
#endif
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