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"
20 class LibShuffCommand : public Command {
23 LibShuffCommand(string);
29 vector<string> groupNames;
32 int printCoverageFile();
33 int printSummaryFile();
35 GlobalData* globaldata;
39 int numGroups, numComp, iters;
40 string coverageFile, summaryFile;
41 vector<vector<int> > pValueCounts;
42 vector<vector<double> > savedDXYValues;
43 vector<vector<vector<double> > > savedMinValues;
46 string outputFile, groups, userform, savegroups, outputDir;
47 vector<string> Groups, outputNames; //holds groups to be used