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();
32 void help() { m->mothurOut(getHelpString()); }
35 vector<string> groupNames;
38 int printCoverageFile();
39 int printSummaryFile();
45 int numGroups, numComp, iters;
46 string coverageFile, summaryFile, phylipfile, groupfile;
47 vector<vector<int> > pValueCounts;
48 vector<vector<double> > savedDXYValues;
49 vector<vector<vector<double> > > savedMinValues;
52 string outputFile, groups, userform, savegroups, outputDir;
53 vector<string> Groups, outputNames; //holds groups to be used