1 #ifndef LIBSHUFFCOMMAND_H
2 #define LIBSHUFFCOMMAND_H
8 * Created by Sarah Westcott on 3/9/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
13 #include "command.hpp"
14 #include "fullmatrix.h"
19 class LibShuffCommand : public Command {
22 LibShuffCommand(string);
26 vector<string> setParameters();
27 string getCommandName() { return "libshuff"; }
28 string getCommandCategory() { return "Hypothesis Testing"; }
29 string getHelpString();
30 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"; }
31 string getDescription() { return "a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic"; }
34 void help() { m->mothurOut(getHelpString()); }
37 vector<string> groupNames;
40 int printCoverageFile();
41 int printSummaryFile();
47 int numGroups, numComp, iters;
48 string coverageFile, summaryFile, phylipfile, groupfile;
49 vector<vector<int> > pValueCounts;
50 vector<vector<double> > savedDXYValues;
51 vector<vector<vector<double> > > savedMinValues;
54 string outputFile, groups, userform, savegroups, outputDir;
55 vector<string> Groups, outputNames; //holds groups to be used