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);
26 vector<string> getRequiredParameters();
27 vector<string> getValidParameters();
28 vector<string> getRequiredFiles();
29 map<string, vector<string> > getOutputFiles() { return outputTypes; }
34 vector<string> groupNames;
37 int printCoverageFile();
38 int printSummaryFile();
40 GlobalData* globaldata;
44 int numGroups, numComp, iters;
45 string coverageFile, summaryFile;
46 vector<vector<int> > pValueCounts;
47 vector<vector<double> > savedDXYValues;
48 vector<vector<vector<double> > > savedMinValues;
51 string outputFile, groups, userform, savegroups, outputDir;
52 vector<string> Groups, outputNames; //holds groups to be used
53 map<string, vector<string> > outputTypes;