8 * Created by westcott on 2/7/11.
9 * Copyright 2011 Schloss Lab. All rights reserved.
13 #include "command.hpp"
18 class AmovaCommand : public Command {
24 vector<string> getRequiredParameters();
25 vector<string> getValidParameters();
26 vector<string> getRequiredFiles();
27 map<string, vector<string> > getOutputFiles() { return outputTypes; }
32 double runAMOVA(ofstream&, map<string, vector<int> >, double);
33 double calcSSWithin(map<string, vector<int> >&);
34 double calcSSTotal(map<string, vector<int> >&);
35 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;