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"
15 #include "fullmatrix.h"
21 class LibShuffCommand : public Command {
29 vector< vector< vector<float> > > cValues; // vector<vector of coverage scores, one for each comparison.> -one for each distance level.
30 vector< vector<float> > deltaValues; // vector< vector of delta scores, one for each comparison.> -one at each distance
31 vector<float> sumDelta; //sum of delta scores, one for each comparison.
32 vector<float> sumDeltaSig; //number of random matrixes with that delta value or ??
33 vector< vector<float> > rsumDelta; //vector< vector<sumdelta scores for a given comparison> >
34 vector<string> groupComb;
39 int findIndex(float, int);
40 void printCoverageFile();
41 void printSummaryFile();
43 GlobalData* globaldata;
47 int numGroups, numComp, iters;
48 string coverageFile, summaryFile, form;