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"; }
26 string getOutputFileNameTag(string, string);
27 string getHelpString();
28 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"; }
29 string getDescription() { return "analysis of molecular variance"; }
32 void help() { m->mothurOut(getHelpString()); }
35 double runAMOVA(ofstream&, map<string, vector<int> >, double);
36 double calcSSWithin(map<string, vector<int> >&);
37 double calcSSTotal(map<string, vector<int> >&);
38 map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
41 vector<string> outputNames, Sets;
43 string outputDir, inputDir, designFileName, phylipFileName;
45 vector< vector<double> > distanceMatrix;
47 double experimentwiseAlpha;