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);
26 vector<string> setParameters();
27 string getCommandName() { return "homova"; }
28 string getCommandCategory() { return "Hypothesis Testing"; }
30 string getHelpString();
31 string getOutputPattern(string);
32 string getCitation() { return "Stewart CN, Excoffier L (1996). Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry). J Evol Biol 9: 153-71. \nhttp://www.mothur.org/wiki/Homova"; }
33 string getDescription() { return "homova"; }
36 void help() { m->mothurOut(getHelpString()); }
39 double runHOMOVA(ofstream& , map<string, vector<int> >, double);
40 double calcSigleSSWithin(vector<int>);
41 double calcBValue(map<string, vector<int> >, vector<double>&);
42 map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
45 vector<string> outputNames, Sets;
47 string outputDir, inputDir, designFileName, phylipFileName;
49 vector< vector<double> > distanceMatrix;
51 double experimentwiseAlpha;