1 #ifndef HOMOVACOMMAND_H
2 #define HOMOVACOMMAND_H
8 * Created by westcott on 2/8/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
14 #include "command.hpp"
19 class HomovaCommand : public Command {
22 HomovaCommand(string);
25 vector<string> getRequiredParameters();
26 vector<string> getValidParameters();
27 vector<string> getRequiredFiles();
28 map<string, vector<string> > getOutputFiles() { return outputTypes; }
33 double runHOMOVA(ofstream& , map<string, vector<int> >, double);
34 double calcSigleSSWithin(vector<int>);
35 double calcBValue(map<string, vector<int> >, vector<double>&);
36 map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
39 map<string, vector<string> > outputTypes;
40 vector<string> outputNames;
42 string outputDir, inputDir, designFileName, phylipFileName;
44 vector< vector<double> > distanceMatrix;
46 double experimentwiseAlpha;