8 * Created by westcott on 2/7/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
13 #include "command.hpp"
16 class AmovaCommand : public Command {
23 vector<string> setParameters();
24 string getCommandName() { return "amova"; }
25 string getCommandCategory() { return "Hypothesis Testing"; }
27 string getHelpString();
28 string getOutputPattern(string);
29 string getCitation() { return "Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\nhttp://www.mothur.org/wiki/Amova"; }
30 string getDescription() { return "analysis of molecular variance"; }
33 void help() { m->mothurOut(getHelpString()); }
36 double runAMOVA(ofstream&, map<string, vector<int> >, double);
37 double calcSSWithin(map<string, vector<int> >&);
38 double calcSSTotal(map<string, vector<int> >&);
39 map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
42 vector<string> outputNames, Sets;
44 string outputDir, inputDir, designFileName, phylipFileName;
46 vector< vector<double> > distanceMatrix;
48 double experimentwiseAlpha;