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#ifndef LIBSHUFFCOMMAND_H
#define LIBSHUFFCOMMAND_H
/*
* libshuffcommand.h
* Mothur
*
* Created by Sarah Westcott on 3/9/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "command.hpp"
#include "fullmatrix.h"
#include "libshuff.h"
#include "groupmap.h"
class LibShuffCommand : public Command {
public:
LibShuffCommand(string);
~LibShuffCommand(){};
vector<string> setParameters();
string getCommandName() { return "libshuff"; }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001). Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67: 4374-6. \nSchloss PD, Larget BR, Handelsman J (2004). Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70: 5485-92. \nhttp://www.mothur.org/wiki/Libshuff"; }
string getDescription() { return "a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
void setGroups();
int printCoverageFile();
int printSummaryFile();
GroupMap* groupMap;
FullMatrix* matrix;
Libshuff* form;
float cutOff, step;
int numGroups, numComp, iters;
string coverageFile, summaryFile, phylipfile, groupfile;
vector<vector<int> > pValueCounts;
vector<vector<double> > savedDXYValues;
vector<vector<vector<double> > > savedMinValues;
bool abort, sim;
string outputFile, groups, userform, savegroups;
vector<string> Groups, outputNames; //holds groups to be used
};
#endif
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